Macs in Chemistry

Insanely Great Science

Wolfram|Alpha and chemistry homework problems

 

There is an interesting post on Molecular Modeling Basics on the use of Wolfram Alpha to solve chemistry homework problems. I have to say I continue to be impressed by Wolfram Alpha, the breadth and depth of science that is covered is amazing.

For science apps for iOS have a look at the mobile science page.

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Anaglyph 3D now available in iMolview

 

I was just reading the end of year newsletter from [Molsoft] and I came across this interesting snippet.

MolSoft is excited to announce that Anaglyph 3D is now available to use in ICM and iMolview.

Sure enough the update on Dec 24th has this in the release notes.

Anaglyph stereo mode is added. (Set 'Stereo Type' to 'Anaglyph' in Tools menu) Any red-cyan 3D glasses will work in this mode.

There are a number of suitable glasses on Amazon 3D Red/Cyan Glasses

I think this is the first app to enable this sort of stereo viewing and it just underlines the strides that mobile platforms are making in scientific computing.

For science apps for iOS have a look at the mobile science page.

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PDBinout

 

Ever had problems with an unusually formatted PDB file? PDBinout is a file conversion tool for PDB files that might interest you. It was created by Tomasz Woźniak at the Laboratory of Structural Chemistry of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences

PDB format is the most commonly used by various programs to define three-dimensional structure of biomolecules. Those programs however, often use different versions of this format. Therefore, it is often necessary to write own re-formatting scripts or change files manually, which makes PDB files less convenient to use. There are only few tools allowing to change one or two versions of PDB format into another and no comprehensive approach for unifying PDB format was developed. Here we present an open-source, Python-based tool PDBinout for processing and conversion of various versions of PDB file format for biostructural applications. Moreover, PDBinout allows to create one’s own PDB versions.

The download also includes a tutorial.

Reference Woźniak T. and Adamiak R.W. (2013) Personalization of structural PDB files, Acta Biochimica Polonica 60, Paper in Press

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iOS7 Tech talks

 

The iOS7 tech talk videos are now online.

Registered Apple Developers can watch full sessions from the iOS 7 Tech Talks to get in-depth guidance on developing for iOS 7. Discover how to create innovative, flexible, and intuitive apps that integrate the latest Apple technologies.

ios7

For science apps for iOS have a look at the mobile science page.

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Papers 3 has just been released

 

The hugely popular reference management application Papers has just been updated. Papers 3 has a new cleaner interface and a host of new features.

Papers3

The mobile app Papers 3 for iOS has also been updated.

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Crunchyard

 

I noticed that CPMD a parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics. is now available on Crunchyard expanding the list of available Computational Chemistry packages. The following packages are also available. CP2K, LAMMPS, GAMESS, GROMACS , NWCHEM

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Export as mol file script updated

 

I’ve added a minor update to the Export as mol file script.

One of the issues with the original script that the mol file contains in its first line the incorrect title of the file (it appears to be the name of the document template).

When you just launched your ChemDraw application, or created a new document, the title would be “Untitled **”, such as "Untitled ACS Document 1996-1". When you save it as Mol file, its header block will inherit the current document title "Untitled ACS Document 1996-2”.

Untitled ACS Document 1996-2
ChemDraw12201318592D

14 16  0  0  0  0  0  0  0  0999 V2000

It would be better to have the molfile title the same as the file name the user enters in the dialog box, one way to achieve this is to “edit” the file and then save again to the same file name. We can do this by adding a line to clean up the structure and then saving.

try
save first document in (molAttachment) as "MDL Molfile”
--This is to ensure the title of the mol file is set correctly
do menu item "Clean Up Structure" of menu "Structure"
save first document in (molAttachment) as "MDL Molfile"
close first document saving no

If you now look at the mol file in a text editor you can see the title is set more appropriately.

Mol file1.mol
ChemDraw12201319082D

14 16  0  0  0  0  0  0  0  0999 V2000
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MacPro in the Applestore

 

When I logged in the morning the first message I noticed announced the eagerly awaited MacPro was now available for order at the AppleStore with delivery on December 30th, within an hour or so that delivery time had changed to January, when I check now the delivery has moved to February. Well at least it is free delivery.

macpro

It will be interesting to see how long it takes Apple to sort out supply and demand.

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Mobile Science Website

It has been just over a month since I set up the Mobile Science database and I thought it would be good to have a look at how things were going. The aim of the database was to enable scientists to be able to search for scientific apps for iOS.

It took a lot of work to compile all the information so I’m delighted to see that it has been accessed nearly 1500 times with visitors from all over the world. A fair number of people have been voting for their favourite application and it perhaps not surprising that the chemical drawing applications, Elemental, ChemDoodle Mobile and ChemDraw are all in the top 5. The other apps picking up votes are popular scientific search and computation tool WolframAlpha and the award winning reference management app Papers3, together with ElementalDB an app that allows you to search a local copy of the 1.2 million record ChEMBL database, an app that really demonstrates the computing power now available in a hand-held device.

I will of course continue to update the database but since finding science apps on the iTunes Store can be a challenge I’d be delighted to hear about any that I have missed.

elemental

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Molecule database framework

 

I thought I would highlight a recent publication I read in Journal of Cheminformatics “Molecule database framework: a framework for creating database applications with chemical structure search capability” Journal of Cheminformatics 2013, 5:48 DOI.

From the abstract

Molecule Database Framework is written in Java and I created it by integrating existing free and open-source tools and frameworks. The core functionality includes:Chemical structure searches combined with property searches. Support for multi-component compounds (mixtures) mport and export of SD-files. Optional security (authorization). For chemical structure searching Molecule Database Framework leverages the capabilities of the Bingo Cartridge for PostgreSQL and provides type-safe searching, caching, transactions and optional method level security. Molecule Database Framework supports multi-component chemical compounds (mixtures). Furthermore the design of entity classes and the reasoning behind it are explained. By means of a simple web application I describe how the framework could be used. I then benchmarked this example application to create some basic performance expectations for chemical structure searches and import and export of SD-files.

While not a drag and drop solution it provides a means to create your own personal chemically searchable database.

Molecule Database Framework is available for download on the projects web page on bitbucket: https://bitbucket.org/kienerj/moleculedatabaseframework.

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pKa Prospector

 

OpenEye have just announced the release of pKa Prospector v1.0 a database of high quality experimental pKa determinations. The ionisation state of a drug molecule can have profound effects on affinity, dissolution, absorption, distribution, metabolism and off-target activity. The ability to predict pKa is often compromised by the lack of relevant experimental data, pKa Prospector is intended to address that issue.

The built-in experimental pKa database was compiled by Tony Slater of pKaData Limited from a collection of IUPAC sources. Each measurement has been individually verified, curated, and assigned a metric of quality. There are more than 30,000 experiments across 12,000 molecules represented. The database is particularly relevant for medicinal chemistry due to the strong preponderance of room temperature aqueous measurements, the many molecules with multiple experimental records, and the presence of over three hundred different heterocycles.

It is also possible to add additional experimental results and have them integrated into the application thus expanding the chemical space covered. The search uses rooted maximum common substructure (MCS) with "electronically-aware" scoring, alternatively it can be searched by similarity or substructure. Ionizable groups are automatically identified and highlighted.

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Export as mol file

 

A number of publishers are seeking to add extra value to publications by including access to chemical structure information to aid searching and indexing. More details are included in this comment from Elsevier.

Elsevier would like to enrich online articles by visualising and providing details of chemical structures you define as the main chemical compounds described in your article. For this purpose, mol files of the key compounds can be uploaded in EES. Please use your preferred drawing tool to export chemical structures as mol files and ensure that they are well defined and do not contain aromtic bonds, R-Groups or other variables. Submitted mol files will be available for downloading from your online article on ScienceDirect. Furthermore, Elsevier will generate InChI keys from the mol files and include them in the online article, which increase the online searchability of your article e.g. in Google. InChI keys will also be used to link the article to additional data in Reaxys.

Since you need to export each structure as an individual file this will become somewhat tedious, fortunately Brian Myers has written an applescript that greatly helps the process for ChemBioDraw users

Now updated.

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Markdown Editors

I’ve just added InkMark to the page of Markdown editors.

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MacBook Pro Upgrade

 

I thinking of upgrading my 5 year old MacBook Pro, in particular I was thinking of installing a solid state drive. I know I can replace the old hard drive but I was wondering if might be possible to replace the DVD drive which I actually never used. Has anyone any experience of this?

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The Elements in Action

 

Originally Theodore Gray produced a beautiful coffee table book The Elements: A Visual Exploration of Every Known Atom in the Universe, this was later converted into an iPad app The Elements which gave access to more dynamic information than could be achieved with a hard copy book. Now the developers have gone one step further and created The Elements in Action a periodic table with video explorations of the properties of elements. Some of the videos look like they have been rescued from old research labs so this is probably your only opportunity to see them in action.

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CH5M3D

 

Whilst there are a number of desktop applications that allow for the creation or editing of 3-dimensional chemical structures there are not as far as I am aware any tools for editing the 3D structure within a web page. CH5M3D uses a combination of HTML5 and javascript to interactively draw and edit 3-dimensional structures of small molecules.

137

The details are described in a recent publication Journal of Cheminformatics 2013, 5:46 DOI, it can be downloaded from Sourceforge, and you can try it out on the CH5M3D website.

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ChemDoodle 6 released

The latest update to the increasingly popular chemical drawing package ChemDoodle has just been released. ChemDoodle 6 is the latest update from iChemLabs and once again it supports Mac, Linux and Windows and works with most document creation packages. This is apparently a free upgrade for those who recently purchased ChemDoodle 5. I plan to write a review of ChemDoodle 6 when I have time but looking at the release notes this looks to be a substantial update.

chemdoodle6

New features in ChemDoodle 6:

  • IUPAC naming with over 20 options!
  • Carbon nanotube and prism builders. Both zigzag and armchair nanotubes can be built. These tools quickly produce 3D geometries.
  • Auto updating labels can now be attached to molecules, so they will update with IUPAC names, molecular formulas and more.
  • Mac OS X Quick Look plugin. Easily preview all your chemical files in Finder just by pressing the space key.
  • More Windows support, including a more powerful tool for supporting Windows filetype associations with the option to unassign types, support for the MDLCT and MDLSK clipboard formats for copying and pasting between a wider array of chemical applications, and greatly improved OLE support to allow for double-clicking to edit structures.
  • More glassware, including a new organized glassware window. You can now also remove liquid from the templates.
  • Significantly improved graphics. Graphics in ChemDoodle were already very good, but we took a look at all the graphics at very high scales and resolutions. We have made sure to focus on all the little details. Bond join edge cases have been improved. Hashes are now auto centered, making recessed bonds and dashed bonds look much nicer. Other bond types have been scrutinized for the best aesthetics. Convex hull algorithms have been built for better placement of bonds around labels. Cis double bonds will now prefer the inside edge. Circles over charges now only surround the number. Aromatic ring circles now meld to the shape of aromatic circles. Arrows look nicer. You won't find better graphics in any other application.
  • 3D coordinate generation.
  • A new 180° chain angle clean option for easily creating Lewis structures and figures with 90° angles.
  • Complex embedded ring systems (like corannulene) now clean very well in 2D.
  • Added resolution controls to the Elemental Analysis widget.
  • Meso stereochemistry support.
  • An advanced formatted text system for the system clipboard. You can now copy and paste your molecular formulas, IUPAC names and others into word processing applications with formatting intact.
  • Many other minor, but useful features: option for the delete key to decrement bonds, nominal mass counter, improvements to the TLC Plate widget, improvements to arc placement previews, alt and shift now modify attribute placement just like placing bonds, improved file chooser previews for data files, more templates for the Templates widget, and more.
  • Squashing of dozens of bugs.

Remember also that there are also ChemDoodle Mobile.

ChemDoodle Mobile, the mobile companion to ChemDoodle, is provided for free to ChemDoodle desktop customers. ChemDoodle Mobile is available for both iOS (iPod Touch/iPhone/iPad) and Android devices. You can transfer structures between ChemDoodle desktop and ChemDoodle Mobile, to take with you into the lab

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Mobile science app updates

 

A couple of applications from Molecular Materials Informatics, Inc have been updated.

Open Drug Discovery Teams is a content management system providing crowd sourced information on a range of tropical and neglected diseases. The ODDT app is free. It can be used anonymously to browse topics. Submission of content requires the user's Twitter account to be enabled and made available to the app.

ODDT

Living Molecules allows specially crafted molecular glyphs to be snapped by the device camera, which direct the app to chemical data: molecules, reactions and collections. This update fixes a bug that could cause the app to crash.

Mobile Molecular DataSheet update includes Sketcher improvements: crayon gestures for adding rings and lines; traversal gesture for growing rings from bonds; and a "band-aid" feature for fixing badly drawn chain bonds.

There is now a searchable database of mobile science apps

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CPMD added to alphabetical listing

I’ve added CPMD to the alphabetical listing of applications.

CPMD is an ab initio electronic structure and molecular dynamics (MD) program using a plane wave/pseudopotential implementation of density functional theory (DFT). It is mainly targeted at Car-Parrinello MD simulations, but also supports geometry optimizations, Born-Oppenheimer MD, path integral MD, response functions, QM/MM, excited states and calculation of some electronic properties.

Full installation instructions are available on the website together with the user manual and examples.

The examples can run effectively on an Intel Core i5 (2.53 GHz, OS/X) with 4 GB of available memory (most of tests require ca. 1GB, few more). Nonetheless, references have been generated on an IBM Blade power7 (with 8 mpi tasks and 1 OMP task per CPMD run) with 64 GB of available memory. Estimates of the execution time and memory requirements will be given based on this more performant setup.

CPMD capabilities

  • Works with norm conserving or ultrasoft pseudopotentials
  • LDA, LSD and the most popular gradient correction schemes; free energy density functional implementation
  • Isolated systems and system with periodic boundary conditions; k-points
  • Molecular and crystal symmetry
  • Wavefunction optimization: direct minimization and diagonalization
  • Geometry optimization: local optimization and simulated annealing
  • Molecular dynamics: constant energy, constant temperature and constant pressure
  • Path integral MD
  • Response functions
  • Excited states
  • Many electronic properties
  • Time-dependent DFT (excitations, molecular dynamics in excited states)
  • Coarse-grained non-Markovian metadynamics

CPMD is free for non-profit organisations.

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Graph-R

 

I’ve just added Graph-R to the page of data analysis tools.

Graph-R is an application used to create 3-dimensional contours, contour lines, wire frames, and scatter diagrams from numeric data files(CSV files). Graph setting is easy. The perspective direction can be freely changed using your mouse. Graph that are created can be saved as PNG or JPEG files.

This software requires Mac OSX 10.8 or later.

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SYBYL-X 2.1.1 released

 

SYBYL-X 2.1.1 is now available, the focus of this release is to extend the capabilities available via the standalone PYTHON interface to 3D-QSAR, which was introduced in SYBYL-X 2.1 earlier this year. The PYTHON API allows 3D-QSAR models (CoMFA, CoMSIA, and Topomer CoMFA) to be created and used for predictions outside of SYBYL-X.

  1. Hologram QSAR (HQSAR) is a now available via Python.  HQSAR has been successfully applied to generate predictive global QSAR models for on- and off-target effects and models for important ADME related properties; the HQSAR method employs 2D-substructural counts as descriptors.

  2. Similarity computations and similarity searches (UNITY 2D fingerprints) are now accessible via Python to support various workflows, such as lead expansion, lead hopping, and cluster analysis.

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Markdown Editors

 

I use markdown extensively on my websites, “Markdown” is two things: (1) a plain text formatting syntax; and (2) a software tool, written in Perl, that converts the plain text formatting to HTML allowing you to build HTML documents in an easily readable form. As the use of Markdown has increased in popularity there are now a wide choice of Markdown editors available for MacOSX and recently iOS so i’ve updated the listing of Markdown Editors.

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Scientific Applications under Mavericks (Update 11)

 

Whilst there are many sites that track the compatibility on common desktop applications, it is often difficult to find out information about scientific applications. Given that this seems to be such a major upgrade I thought I’d set up a spare machine to test applications before I update my main machine.

The update went smoothly albeit with an overnight download of the 5.5 GB file.

The update removes both X11 and java so both of these need to be reinstalled, if you forget you will be prompted to download the first time you try to use them.

No issues with cursory testing, users or vendors provided feedback

Avogadro
BBEdit
ChemDoodle
ChemSpotlight
Cresset software (forge, torch, spark) (no reported issues)
Elemental
FTranProjectBuilder
iBabel
ICM-Pro
ICM-Homology
ICM-VLS
ICM-Chemist
iNMR (No reported issues)
Matlab
Marvin
MOE
Openbabel
OpenEye (Command line tools OK, OMEGA 2.5.1 (OSX 10.8 version), FILTER 2.5.1 (10.8), ROCS 3.2.0 (10.8), SZMAP 1.2.0 (10.8), EON 2.2.0 (10.8), QUACPAC 1.6.3 (10.8), SZYBKI 1.8.0 (10.8), FLYNN 2.3.0 (10.8), The Python and Java toolkits work fine. The C++ toolkit can be made to work if some of the compiler flags are changed. Please email support@eyesopen.com for more details. For the OpenEye GUI applications, vROCS 3.2.0 (OSX 10.8 version) works fine, for other apps see below
R latest version R 3.0.2 ("Frisbee Sailing")
Reference Tracker
StarDrop
Vortex
XQuartz

Some issues :-(

MOE install
I downloaded the latest update as a zip file and unarchived it. When I double click on the installer I got a message that it was broken or corrupted. This seems be an issue with the Mac OSX Gatekeeper,

  1. Open Apple menu, then go to System Preferences -> Security & Privacy -> General tab.

  2. In the option list of "Allow Applications downloaded from", select "Anywhere".

Then installs OK. Once installed MOE seems to run fine.

CCDC Software
Mac OSX 10.9 causes most CCDC software to fail - there are now have patches available that address this issue. For enCIFer 1.4: http://www.ccdc.cam.ac.uk/SupportandResources/Downloads/pages/ProtectedDownloadAgreement.aspx?d=15 For the 2013 CSD System go to: http://www.ccdc.cam.ac.uk/SupportandResources/Downloads/pages/ProtectedDownloadAgreement.aspx?d=47  For standalone Mercury 3.1 or 3.1.1 go to:  http://www.ccdc.cam.ac.uk/SupportandResources/Downloads/pages/ProtectedDownloadAgreement.aspx?d=37
These updates should only be applied on Mac OSX 10.9. NB One reader reported issues with the update.

ChemBioDraw
Chemdraw 13 files pasted into Keynote 6 cannot be copied and pasted back into ChemDraw. In addition, if you open old Keynote files in Keynote 6 all the ChemDraw cannot be copied and pasted. It pastes into Chemdraw as a picture with an all black background. In Mac OS 10.9 with Keynote 5 - round trip editing still continues to work. According to the PerkinElmer Support Forum there are issues with copy/paste in CD 13 to Office 2011 for Mac. Any CD structures that are pasted into PPT or Word cannot be opened or edited with CD.

EndNote X7
We have tested EndNote X7 with Mac OS X 10.9 Mavericks to determine compatibility. We have found some minor issues and are working on a free update patch to be released in the next few weeks.

EndNote X6
EndNote X6 is not officially compatible with Mac OS X 10.9 Mavericks. We are testing EndNote X6 with Mac OS X 10.9 Mavericks to determine informal compatibility and will report any exceptions found on this page.
EndNote X5 and earlier
Due to major compatibility issues, it is not recommend to attempt to use EndNote X5 or earlier on OS X 10.9. When attempting to launch EndNote X5 or earlier, a warning message comes up that will include "unable to load ....ENCore.Bundle". EndNote X5 and earlier will fail to launch after receiving this message. There are no known workarounds for this issue besides moving to a more recent version of EndNote or restoring your computer  (using a Time Machine Backup for example) to a previous version of Mac OS X.

OpenEye Command line tools that require setting the OE_ARCH environment variable (FRED 3.0.1 (OSX 10.7 version), HYBRID 3.0.1 (10.7), POSIT 1.0.3 (10.7), LEXICHEM 2.1.0 (10.6), BROOD 2.0.0 (10.5)

export OE_ARCH=osx-10.9-x64:osx-10.8-x64:osx-10.7-x64:osx-10.6-x64:osx-10.5-x86

For the OpenEye GUI applications, vROCS 3.2.0 (OSX 10.8 version) works without any issues. VIDA requires the OE_ARCH modification shown above but also needs the following additional fixes:

sudo mkdir -p /Applications/OpenEye/arch/osx-10.6-x64/vida/4.2.1/bin/QtCore.framework/Versions/4
sudo ln -s /Applications/OpenEye/arch/osx-10.6-x64/vida/4.2.1/bin/QtCore /Applications/OpenEye/arch/osx-10.6-x64/vida/4.2.1/bin/QtCore.framework/Versions/4/QtCore

Unfortunately, the current vBROOD, AFITT, and MAKE_RECEPTOR GUIs do not work on Mavericks. We are actively investigating these issues. More details

Using Aabel v3 on Mavericks is not recommended due to cosmetic glitches such as misalignment of graphic viewer icons on the Mavericks buttons. Mavericks will be supported in the next major version of Aabel

Papers2 update about to be released

If I hear of anything, I’ll update this page.

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Chem3D and ChemDraw for iPad updated

 

Both ChemDraw and Chem3D have been updated, the release notes don’t give much information on the updates other than Redesigned for iOS7 and bug fixes.

The use of mobile devices in teaching has offered new opportunities and a recent presentation by Layne Morsch illustrates this quite nicely. Using ChemDraw for iPad and Flick-to-Share to Increase Engagement in Organic Chemistry. The page has a couple of embedded videos that give more details.

The other feature that is now becoming mainstream is the 3D-printing and since Chem3D can export in .stl format it is not surprising people have started to experiment with creating 3D models of molecules, there is a brief video here, unfortunately it is a loop of the printing process so don’t expect to see the final product. CambridgeSoft have also produced their own videos of these apps in action

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Mobile Science App updates

 

A couple of apps have been updated recently

WolframAlpha the world's definitive source for instant expert knowledge and computation.

Living Molecules allows specially crafted molecular glyphs to be snapped by the device camera, which direct the app to chemical data: molecules, reactions and collections

There is now a database of mobile science apps

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ASObjC Explorer updated

 

I just saw this message from Shane Stanley

As some of you have probably found already, Xcode does not recognize AppleScript's new interleaved syntax when used for action handlers -- you cannot make connections to them from controls. The workaround is to keep using the underscore syntax for action handlers until the problem is resolved. That's not ideal if you use an external editor, though. FYI, I've just released a new version (3.0.7) of ASObjC Explorer for Mavericks to deal with this issue. There is a new preference setting in Preferences -> Other. When checked, every time you save a .applescript file, any single-argument handlers will be changed to use old-style underscore syntax. (The new syntax will appear in Xcode and in the saved file, while the new syntax will still appear in Explorer.)

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XQuartz Updated

 

XQuartz has been updated this contains X11 2.7.5 the first release supported on Mavericks. Full details are available here

The XQuartz project is an open-source effort to develop a version of the X.Org X Window System that runs on OS X. Together with supporting libraries and applications, it forms the X11.app that Apple has shipped with OS X since version 10.5.

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Bug in ChemBioDraw.

 

There was a blog entry on In the Pipeline about a bug in ChemDraw. Actually this has been known for a while (and present in previous versions) but it seems it still has not been fixed in the latest version of ChemBioDraw 13 on the Mac. As you can see in the image below including explicit hydrogens in your structure significantly impacts the calculated LogP. Whilst people don’t often add explicit atoms to phenyl rings, (expect perhaps in SAR studies) they often add them to heteroatoms.

temp22

At the moment there is no bug fix and no date set for a fix to any version of ChemBioDraw, the only approach is to avoid adding explicit hydrogens to structures if you want to calculate LogP. I’ve looked at a number of other applications and there seem to be no issues with ChemDoodle, Elemental, Marvin or OpenBabel.

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Graph Builder

 

I just got a message about an update to Graph Builder a very popular and powerful application from VVimaging, Inc rich in graphic editing, creation and programming to facilitate the visualization of information. It has a excellent complement of 2D and 3D graph features, a full-fledged user interface and is programmable. Paste data into table editors, write scripts to generate data, load a Xcode plugin you write for data generation and to retrieve data from external sources. Also supports dynamic graphs.


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iOS programming

 

As the MobileScience site expands I’ve started to add other resources in addition to the applications. There are now a couple of useful additions for iOS programmers if you are looking for a training course, a plotting library or a chemistry toolkit.

I’d be delighted to add any more useful resources.

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ChemmineOB

 

ChemmineOB provides an R interface to a subset of cheminformatics functionalities implemented by the OpelBabel C++ project. OpenBabel is an open source cheminformatics toolbox that includes utilities for structure format interconversions, descriptor calculations, compound similarity searching and more. ChemineOB aims to make a subset of these utilities available from within R. For non-developers, ChemineOB is primarily intended to be used from ChemmineR as an add-on package rather than used directly.

More details here

Comments

Supercomputer plans

 

An interesting article on plans to build a supercomputer based on cellphone chips. It seems the low power consumption of ARM processors make construction of a supercomputer based on those chips an attractive proposition.

Wired Article

His project is part of a larger movement towards this new breed of low-power chips. As Ramirez builds an ARM supercomputer in Spain, web giants such as Facebook and Amazon are exploring the use of these low-power chips in the servers that run their massive online services.

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MobileScience Apps

Finding scientific applications for your iPhone to iPad has always been a little hit and miss since there is no “science” category on the iTunes store. To help out I created a page listing applications that I knew about, unfortunately as the number of applications increased the page became unmanageable. In addition an alphabetical listing is not the most useful way to search through them.

I’ve now transferred all the information to a database that can be searched via a web interface.

mobsci

The site is available at http://www.macinchem.org/mobilescience/, I’ve started to categorise applications to aid navigation but I’d be interested to hear of any suggestions. Currently there are over 200 entries covering an extensive area of science, if I’ve missed any please let me know and I’ll add them.

In the news section I’ve added links to publications and presentations that might be interesting.

I’d encourage to have a look around and I’d be interested to hear any comments or suggestions.

 

Comments

SZYBKI has been updated

 

OpenEye have just released an update to SZYBKI with a host of new features. SZYBKI is used to optimise the three dimensional structure of molecules prior to their use in other programs. SZYBKI also refines portions of a protein structure and optimize ligands within a protein active site, making it useful in conjunction with docking programs.

  • New utility program called FreeForm is available for Szybki users. It provides two distinct functionalities: evaluation of the solvation free energy of the input molecules and free energies of solution conformations. Please Note: FreeForm is not available under 32-bit Windows because of the high memory requirements of this application.
  • A new forcefield for protein-ligand interations is available upon selecting a new option -ff followed by AmberMMFF94 or AmberMMFF94S. It is a combination of MMFF94 (or MMFF94S) with Amber. In this combined force field, MMFF94 (or MMFF94S) is used to describe the intramolecular interactions of the ligand and the Amber force field is used for the VdW and Coulomb interactions between ligand and protein. Currently, this force field can be used only for ligands inside rigid proteins.
  • Entropy estimation based on analytical MMFF Hessian is extended for ligands bound in a rigid protein using the option -entropy.
  • Constraining torsion potential in the form: f8ebfd663514a377a56dfefaeb661230a663dc0f, where 81251f7be3a3c36e3c6602884accebe2d6ab3292 is the user specified force constant and 6b57c4a2f949d360120e9eec70ed44786c71b408 is the reference torsion dihedral angle is available with the use of the input flag -tor_constr.
  • New option -optMethod is introduced for optimization method selection. The possible choices of optimizers type are BFGS, conjugate gradient, steepest descent and mixtures of steepest descent preoptimization followed by BFGS of conjugent gradient. Option -conj is no longer supported.
  • Optimization of molecular systems with large number of degrees of freedom (>= 500) is by default done with the conjugate gradient method unless specifically requested with the option -optMethod.
  • New option -optGeometry is introduced for selection of coordinate system to be used during optimization. It replaces no longer supported options -optcart, -opttorsions, -solid and -noopt. It can be also used to optimize hydrogen atoms positions only, instead of using for that purpose -fixsmarts.
  • Molecules from the input file which failed during processing are by default written to the separate molecular file. See the description of new option -keepFailures.
  • Starting from this release flags -fixsmarts and -harmsmarts are followed by the name of the text file containing a single line with a SMARTS pattern used to fix or constrain atoms. Input of SMARTS strings on the command line for those flags are not used anymore because some SMARTS strings may contain special characters which may be interpreted incorrectly on some platforms.
Comments

Reference Tracker Updated

 

The popular reference management package Reference Tracker) has been recently updated and fully supports Mavericks.

Improved ISBN lookup. Improved article search.

Fixed a bug where incomplete reference styles could be shared to the cloud. Fixed a bug where ISBN lookup results could be imported with missing data. Fixed a bug where open link buttons in documents could reposition incorrectly when the document window was resized. Fixed a bug that could cause Reference Tracker to crash on startup on OS X 10.7. Fixed tabbing between fields in the Publication Search sheet.

I also note that there is a special offer at the moment

Reference Tracker is available at a special 30 % discounted price until 30 November 2013!

There is a list of reference management applications for Mac OS X here.

Comments

Marvin 6.1.3 released

 

ChemAxon have released a new update to Marvin.

Bugfixes MarvinSketch GUI MSketchPane setPiece(Molecule) method did not work, it set the molecule on the canvas instead of putting it on the cursor. Import/Export CXSMILES/CXSMARTS CXSMARTS containing valence property information was recognized and read as SMARTS. SKC Some reaction was read as R-definition from SKC format.

Comments

Speakable workflows

 

I just learned of an interesting site that is currently under construction. Speakable-Workflows has a number of tutorials on how to use the new speech recognition features in automator actions.

Well worth spending a few minutes watching the video tutorials.

Comments

Applescript and GUI in Mavericks

One of the big changes with Mavericks is the enhanced security and this has an impact on all developers even those who write a “simple” applescript to avoid a tedious or repetitive series of actions.

Developers have often relied upon AppleScript’s ability to control the user-interface, to provide an automation solution when no direct scripting support of an application or process was available. While this valued ability continues to be fully supported in Mavericks, the enhanced security focus of the new OS requires a few changes in how scripters access and apply the Accessibility frameworks.

There is a really comprehensive discussion of Accessibility Preferences and GUI Scripting over on Mac OS X Automation. Well worth a read.

Comments

FTranProjectBuilder

 

I’ve just updated the listing of Scientific Applications under Mavericks and I thought I’d highlight one application. The page I have on Tools for Fortran Programmers is consistently one of the top accessed Blog entries. I’m sure one of the reasons for this popularity is FTranProjectBuilder the only Mac-native Fortran development environment (IDE) it works with the gfortran, g95, ifort, Absoft Pro Fortran, NAG nagfor and PGI pgfortran compilers. Since I mentioned it last FTranProjectbuilder has been updated six more times, in April, May, July, August and October with new features like the ability to build static libraries, trackpad interaction and compiler errors now being marked in the source code. Full details are in the project notes on the Nocturnal Aviation Software website , and yes, all of the tools, including FTranProjectbuilder are compatible with 10.6.8+, and run fine on 10.9 Mavericks. 

Fortran still has a significant user base in the scientific community where the speed, portability, array handling and access to shared memory make it a very powerful option.

There is a nice comparison of programming languages from the viewpoint of scientists here

Comments

GenomeBrowse

 

I’ve just been sent a link to GenomeBrowse, this allows the user to explore DNA-seq and RNA-seq pile-up and coverage data in an intuitive manner. Whether viewing one file or many, an integrated approach is taken to exploring your data in the context of rich annotation tracks. Features include: * Zooming and navigation controls that are natural as they mimic panning and scrolling actions you are familiar with. * Coverage and pile-up views with different modes to highlight mismatches and look for strand bias. * Deep, stable stacking algorithms to look at all reads in a pile-up zoom, not just the first 10 or 20. * Context-sensitive information by clicking on any feature. See allele frequencies in control databases, functional predictions of a non-synonymous variants, exon positions of genes, or even details of a single sequenced read. * A dynamic labeling system which gives optimal detail on annotation features without cluttering the view. * The ability to automatically index and compute coverage data on BAM or VCF files in the background.

GenomeBrowse integrates with the powerful Golden Helix SNP & Variation Suite (SVS) analysis platform. SVS can be used to build custom annotations and perform variant analysis, while GenomeBrowse can visualize findings and validate the evidence for putative variants.

Comments

Regress+2.7.1

 

The free univariate data modeling package Regress+ has been updated to version 2.7.1.

Regress+ offers:-

  • Plain textfile input
    • Equations, with or without uncertainties (weights)
    • Distributions, continuous or discrete data
    • Discrete data grouped or ungrouped
  • Datasets up to 4,294,967,295 points (minimum 7)
  • Up to 10 parameters
  • User-selected optimization criterion (where appropriate)
    • Least squares
    • Minimum average abs(residual)
    • Maximum likelihood
    • Minimum K-S statistic
    • Minimum chi-square statistic
  • Full, dated Report (textfile)
  • Robust goodness-of-fit testing for distributions
    • Tunable precision
  • [Optional] State-of-the-art (BCa) central confidence intervals (90, 95 and 99 percent)
    • Tunable precision
  • High-quality (PDF, PNG) plots with one keystroke!
    • X/Y plot, with or without error bars
    • PDF plot
    • CDF plot
    • Probability plot for goodness-of-fit (see above)
    • [Optional] Logarithmic axes (when appropriate)
    • Editable axis labels
    • Automatic tick marks/labels (see above)
  • [Optional] Predictions for unobserved values or percentiles
    • With confidence intervals if desired
  • [Optional] Constant parameter(s)
  • 21 Built-in Equations
    • Plus user-defined model
    • [Optional] Test residuals for systematic error
    • [Optional] List data with fitted estimates and residuals
    • [Optional] Simulated-annealing mode for initial parameter estimates
  • 59 Built-in Distributions
    • 9 continuous, symmetric
    • 27 continuous, skewed
    • 11 continuous mixtures
    • 6 discrete
    • 6 discrete mixtures
    • [Optional] Creation of synthetic samples
  • No hidden assumptions anywhere
    • No approximations, apart from those common to sampling and bootstrapping generally
    • No data transformations of any kind
  • Extensive documentation

There is comprehensive listing of Mac OSX data analysis packages here.

Comments

Mavericks adoption rate

 

I’ve been looking at the rate of Mavericks adoption here currently it stands at 13-15% which is quite impressive. Interestingly most of the early adopters seems to be those running Mountain Lion, the numbers using Lion and Snow Leopard seem to be pretty much unchanged.

I’ve also updated the post regarding Scientific Applications under Mavericks, if anyone has any more comments I’ll continue to update the page.

Comments

ASObjC Explorer for Mavericks Released

 

Myriad Communications has released its successor to AppleScriptObjC Explorer, available immediately. The new editor takes advantage of the improvements to AppleScript in the latest release of OS X, which make access to Objective-C frameworks from AppleScript easier than ever.

"The changes to AppleScript in Mavericks have largely flown under everyone's radar, but script libraries open lots of doors for scripters," says the application's developer, Shane Stanley. "Bridging between AppleScript and Objective-C code has become much easier. This sets a new direction for expanding AppleScript's abilities."

ASObjC Explorer for Mavericks is designed to make developing AppleScriptObjC-based script libraries simple, with everything you need in one window. It features customised syntax formatting to take advantage of the new interleaved syntax; intelligent code-completion and shortcuts to take the tedium out of entering code; logging, stepping and breakpoints to aid in debugging; and a built-in simplified scripting-definition editor for adding English-like terminology.

It also makes an ideal external editor for AppleScriptObjC-based Xcode projects in Mavericks

ASObjC Explorer for Mavericks can be downloaded from <http://www.macosxautomation.com/applescript/apps/explorer.html>, and can be used free for 30 days. The purchase price is $US49.95.

For further inquiries, contact Shane Stanley at <sstanley@myriad-com.com.au>.


Comments

Marvin 6.1.2 released

 

New features and improvements

  • MarvinSketch Dialog
  • 'Zoom to scaffold' checkbox option has been added to the "Preferences>Save/Load" tab. Documentation
  • Structure Checker
  • External structure checker configuration file URL can be set via Java System Property.

Bugfixes

  • Editing
  • Electron-flow arrow could not be drawn from the A-B bond to the incipient A-C bond of an A-B-C structure. Forum
  • Import/Export
  • MolInputStream and MolImporter could have different format options.
  • MolImporter did not close its inputstream when an exception was thrown in the constructor.
  • MOL, SDF, RXN, RDF
  • Molecule type property was allowed in SDF, CSSDF export.
  • The coordinates of the sequence residue imported from SCSR MOL files were wrong if the residue had three attachment point.
  • CDX/CDXML
  • Color and text format of atom label is exported to CDX and imported from CDX and CDXML. Forum
  • Graphical brackets were not imported from CDX files.
  • Gaussian Z-matrix input format
  • Command line, title line, and extra input properties were not exported to Gaussian Z-matrix input format. Forum
  • Clean 2D
  • Cleaning of position variation bonds could create overlapping bonds.
  • Cleaning of bridged systems could result in overlapping atoms. Forum
  • Calculations
  • Topology Analysis
  • Missing method has been added: TopologyAnalyserPlugin.getFsp3(). API Documentation
  • logD
  • New logD training documentation has been added. Documentation
  • Structure Checker
  • Fixer options in MarvinSketch are updated with newly defined settings.
  • External checkers can be loaded from JAR file in case the JAR file contains a space.
Comments

MOE 2013.08 Released

 

Chemical Computing Group have just announced the release of the latest update of MOE (Molecular Operating Environment).

General Updates

Extended Hückel Theory for Pharmacophore Discovery

  • Apply EHT strengths to identify and discover weak and strong interactions
  • Annotate non-standard interactions: halogen and CH bond donors
  • Score pharmacophore hits using sum of interaction energies

de novo Loop and Linker Modeler

  • Search and browse for de novo and knowledge-based loop candidates
  • Generate multiple loop conformations and score loop-loop interactions • Investigate linkers for fusion proteins and dual variable domains

Protein Alignments and Superpositions

  • Superpose protein structures independent of sequence
  • Apply new threading methodology for sequence to structure alignments
  • Align sequences and superpose structures using STOVCA criteria

Core System Enhancements (with 64-bit support) The default versions of MOE for Linux, Windows, and Mac OSX are now all 64-bit. The current release also includes 32-bit versions for each architecture.

  • Create additional data grouping level in System Manager
  • Handle large number of protein:ligand complexes in real-time
  • Colour database viewer text and cells by data values for enhanced analysis, Empty cells can be specially colored

Interface to Mogul from CCDC

  • Access a knowledge-based library of small molecule crystallographic data
  • Visualize histograms and statistics fo rbond angles, dihedrals and torsions • Ensure ligand conformation is consistent with the CSD

Solvent Analysis using 3D-RISM Enhancements

  • Calculate water densities on full protein or protein:protein interface
  • Accurate placement and stability prediction of water sites
  • Use3 D-RISM densities to validate water position in crystal structures

chEMBL Library. MOE's SD Pipeline Command Tools were used to generate fragments from Release 14 of the ChEMBL database of bioactive drug-like small molecules. The resulting database of conformations, chemblr14_frag.mdb, for approximately 830,000 fragments, suitable for Scaffold Replacement or combinatorial chemistry methodologies

Mac OS X Enhancements.

  1. OS X Dock Icon Enhancements. A new Dock menu, accessed by right-clicking (or control-clicking) the MOE Dock icon, allows for standard Mac OS X operations – Hide, Show, and Quit – across all open iterations of MOE. The Dock Menu also contains menu items in order for users to view the About panel bundled in MOE, as well as access the Preferences panel. Additionally, the Dock indicator light under the MOE Dock icon remains persistent after having launched a new instance of MOE, until all opened MOE instances have been closed. Users continue to be able to drag and drop compatible MOE documents (i.e. .pdb, .svl, etc.) onto the Desktop and/or Dock icons for direct opening in MOE.

  2. New Preferences Menu. A new Preferences panel allows for certain parameters to be set and/or changed graphically. These parameters include the defaults key and path to MOE, the current configuration of MOE (32- or 64-bit, or Auto-select), as well as a selection of common command line tags, with a custom section for inputting other command line options.

  3. Output Continuity. stdout and stderr received from MOE have been standardized to be displayed in a native panel in a scrollable text box.

Comments

Experimental Assistant

 

Experimental Assistant from Nano3D Biosciences. This application helps organize and analyze data from experiments. It take manual photos and automatic shooting for multiple images and time lapse movies, and stores them in albums for easy access later

Comments

ChemDraw and Chem3D for iPad updated

 

There are updates to both ChemDrawand Chem3D) for iPad. There is little information available about the update to version 2.0 other than “bug fixes” and the apps have been redesigned for iOS7 and now have a minimum requirement for IOS7.0 or later.

c3dipad

The mobile science page contains a listing of science apes for iOS.

Comments

Dashboard Widgets

 

A reader just pointed out that the support site for a couple of the items on the widgets page is no longer available.

The Amino Acid Table widget
The Genetic Code widget
The Nucleic Acid Nomenclature widget
The ProtParam widget

Whilst the widgets are still available from a number of download sites the support site "http://www.aborygen.com/" domain is labelled as for sale.

Comments

R update

 

I just noticed that there is an update to R on the CRAN website

This binary distribution of R and the GUI supports 64-bit Intel based Macs on Mac OS X 10.6 (Leopard) or higher. Since R 3.0.0 the binary is a single-arch build and contains only the x86_64 (64-bit Intel) architecture. PowerPC Macs and 32-bit Macs are only supported by building from sources or by older binary R versions. The default package type is "mac.binary" and the binary repository layout has changed accordingly.

There is a listing of data analysis packages for Mac OS X here.

Comments

Scripting Vortex 16

 

OCHEM is a free open access site of annotated models and chemical data. OCHEM contains 1831772 experimental records for about 477 properties collected from 12457 sources you are free to upload your own data and also build predictive models using existing or your own data.

There are also a number of already built models that the public can access, these include

  • Ames test
  • CYP1A2 inhibition
  • LogP and Solubility

You can run predictions on OCHEM using simple REST-like web services, these vortex scripts submit tasks to the various models and then retrieve the resulting prediction.

Comments

Repeater

 

If you want to automate a process but don’t want to learn Applescript then Repeater may be of interest.

Repeater provides a much needed and very convenient platform for recording repetitive actions without having to learn and understand Automator or AppleScript, which are well beyond most user's abilities. Moreover, not all apps can be scripted at all, but Repeater can help you anyway. Furthermore, you can integrate Repeater with popular scripting languages to dramatically improve their possibilities. Repeater is a tool specially designed for recording and playback user actions such as mouse movements and clicks, standard and hardware keystrokes, vertical and horizontal scrolling & zooming. It is also capable of storing information about currently running applications to launch them on playback.

There are also some scripting capabilities for more advanced use. Looks like it could be useful for giving demonstrations.

Comments

SeqAn

 

I’ve recently been sent details of SeqAn, an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. It is released under BSD/3-clause license and is supported under Mac OS X: GNU/g++, LLVM/Clang (3.0+).

Andreas Döring, David Weese, Tobias Rausch and Knut Reinert. SeqAn an efficient, generic C++ library for sequence analysis. BMC Bioinformatics, 9:11, 2008. DOI

Comments

Mobile security concerns

 

I’m hearing more and more concerns about security concerns with regard to mobile devices. I guess this was to be expected as more people have smart phones and tablets start to replace laptops. It seems Google's executive chairman Eric Schmidt drew laughter when discussing security on the Android platform, Executive chairman dances around straight answer while talking up Android security.

Schmidt said in the distant future there would be an assumption that nothing is secure and that security will be devised on a per app basis for each user.

I’m not sure whether many people would find that situation very helpful. His view is perhaps a consequence of a recent study issued by the Department of Homeland Security (DHS) and the Federal Bureau of Investigation (FBI) suggesting Android devices represent a significant security threat. Of the malicious attacks documented in the study, 79 percent took place on an Android device and 19% on Symbian whilst Apple's iOS received just 0.7 percent of the recorded malware threats. One of the key sources of threats appear to be the installation of apps from insecure sites, so whilst the approval process for the Apple iTunes store occasionally causes complaints it also acts as a significant security barrier. Whilst the Google Android should have the same role it is perhaps worrying to find that recently 50 malicious apps had to be removed. There have however now been reports of threats distributed via email spam.

The Android trojan known as Stels began distributing via fake U.S. Internal Revenue Service-themed emails, using an Android crimeware kit to steal sensitive information from the device, and monetizing by making calls to premium numbers.

Apple does seem to be taking the security concerns seriously, the AppStore provides an initial check on apps, the new fingerprint authentication provides an extra level of device protections. In iOS7 we have Activation Lock so that someone who’s got hold of your device can’t disable Find My iPhone without knowing both your Apple ID and that Apple ID’s account password. The person with your lost device can’t erase data on the device, also if you designate your device as being lost it can’t be restored to reactivate it—the phone displays only a phone number and a custom message about contacting you.

Keeping the operating system up to date helps, and the adoption rate for iOS7 is very impressive.

Comments

Turning up the heat with Torch and Forge

 

Anyone involved in a drug discovery programme will be aware of the challenge presented by trying to visualise and explore structure-activity relationships (SAR), in particular visualising questions like :-

“What is the largest change that can be made whilst maintaining activity?”

Activity Miner from Cresset is a new tool designed to rapidly interrogate and decipher SAR in both Torch and Forge. Activity Miner is intended to help identify key elements of the SAR by starting from a set of aligned molecules and then automatically comparing them to each other.

Activity Miner1

More details are here

Comments

More Markdown editors

 

I use markdown extensively on my websites, “Markdown” is two things: (1) a plain text formatting syntax; and (2) a software tool, written in Perl, that converts the plain text formatting to HTML allowing you to build HTML documents in an easily readable form. I mainly use BBEdit and regard it as the “gold standard” but I keep an eye out for other markdown editors and wrote a summary of my findings, I’ve just been sent details of two more apps.

Eratois a simple Markdown editor for the Mac. It is fast, extremely easy to use and gets out of your way. It offers full support for both regular Markdown syntax, GitHub flavoured markdown and YAML front matter.

Marked2 is a previewer for Markdown files. Use it with your favourite text editor and it updates every time you save.

I’ve added them to the summary page.

Comments

Graph Builder updated

 

Graph Builder has been updated

  • Added data input for 2D vector field presentation.
  • Added programmed and animated 2D vector field palette.
  • Updated script documentation for 2D vector field animation and programming.
  • Added a preference option to turn on the built-in network graphing server.
  • Added ability to display dynamic and programmed Graph Builder document results over the web.
  • Updated the manual to explain new features

There is a listing of data analysis applications for Mac OSX here.

Comments

ROCS Updated

 

OpenEye have just announced that the virtual screening tool ROCS v3.2 has been released.

Several noteworthy features have been added to this version including a -subrocs option that can drastically improve substructure alignments. Also included is an application rocs-report that uses our 2D depiction technology to make pdf reports of hitlists displayed with 2D similarity, shape and color overlaps, as well as property histograms. Substantial upgrades have been made to vROCS. An improved sketcher now highlights unspecified stereochemistry in atoms and bonds in query structures, and requires the user to correct any unspecified stereochemistry.

ROCS is available for download here.

Comments

Updated Applescript Resources

 

I’ve just updated the Applescript Resources page, in particular I’ve included updates to the great tools provided by Satimage-Software. These include Smile a programming and working environment that you can use in a variety of situations. You may want to perform a scientific work, to handle cgi requests, to automate an intensive file processing task, to produce computed graphics, to edit XML files, to work with Unicode texts, to make GUI of your scripts, and SmileLab the SmileLab license adds the data visualization features to Smile, the automation environment by Satimage-Software.

smilelabhome

In SmileLab you can

  • extract data from files (default data formats supported: text, binary, FITS, XNF, ...),
  • perform data processing using commands provided with Smile or controlling external code
  • visualize your data in the most usual forms (curves, scatter plots, bar graphs, contour lines, color maps and vector fields in 2D, and 3D surfaces),
  • customize the interaction of the user with the plots (handling mouse clicks, contextual menus, keyboard events...) and create custom interfaces,
  • export your plot as a PDF file, as a bitmap picture (PNG, JPEG, TIFF, BMP, PSD) or as a QuickTime movie.


Comments

OpenCL training course

 

Simon McIntosh-Smith has just released a new OpenCL training course “HandsOnOpenCL" via Github. It Includes a comprehensive set of exercises and solutions in C, C++ & Python.

There is a list of GPU-accelerated scientific applications here.



Comments

iOS7 Adoption rate

 

I was just looking at the iOS7 adoption rate on the Mixpanel website. When I looked last night, iOS7 stood at 63% of users, iOS6 just over 32% with older versions of iOS below 4%. Given that iOS7 has only been available just over a week this is a remarkable adoption rate. Excellent news for all those mobile science developers since it looks like will be able to focus their efforts on the latest version of the operating system,.






Comments

StarDrop 5.4

StarDrop was recently updated to version 5.4, this brings an update to the virtual library design module and scaffold based design, there have also been improvements to the plotting and data visualisation.

There are now seven optional plugins with three exciting new options.

Derek Nexus™ - Knowledge based toxicity prediction The new Derek Nexus module for StarDrop provides Lhasa Limited's world-leading technology for knowledge-based prediction of key toxicities. Using data from published and donated (unpublished) sources, Derek Nexus identifies structure-toxicity relationships that alert you to the potential for your compounds to cause toxicity. The Derek Nexus module provides predictions of the likelihood of a compound causing toxicity in over 40 endpoints, including mutagenicity, hepatotoxicity and cardiotoxicity.

BIOSTER™ - A world of chemistry experience BIOSTER is developed and updated in collaboration with Digital Chemistry and is available as an optional extension to StarDrop's Nova module. This combination enables you to quickly and easily search the comprehensive BIOSTER database to identify transformations that are relevant to your compounds. These can be automatically applied to generate novel structures with a high likelihood of biological activity and synthetic accessibility, prioritised against the property profile you require for your project. BIOSTER brings the collective experience of the chemistry community to help you to discover new active analogues of your compounds based on the tried and tested principle of isosterism. The BIOSTER module contains a unique compilation of over 20,000 precedented bioisosteric transformations, manually curated from the literature by Dr István Ujváry, complete with references to the original publications in which they are described.

torch3D™ The renamed torch3D module, using Cresset’s unique Field technology to understand and apply 3D Structure Activity Relationship (SAR), has been updated to include the latest version of Cresset’s XED force field providing insight into compounds’ 3D structures, biological activities and interactions.

These certainly significantly expand the potential utility of StarDrop, but note that these are not part of the standard install and may require additional licensing.



Comments

ORCA updated

ORCA is a modern electronic structure program package written by F. Neese, with contributions from many current and former coworkers and several collaborating groups. The binaries of ORCA are available free of charge for academic users for a variety of platforms. ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.

New Features of Version 3.0: 

  • Improved efficiency in integral evaluation and digestion, thanks to Ed Valeev for the improved libint 2.0 library!
  • Improved parallelization, in particular for RI-DFT calculations.
  • The DLPNO-CCSD(T) near linear scaling local correlation method. It has led to the first CCSD(T) level calculation on an entire protein.
  • Explicitly correlated (F12) MP2 and coupled cluster methods using several approximations to boost the efficiency (They also work together with DKH/ZORA, COSMO etc.). Again many thanks for Ed Valeev for his countless contributions to this project.
  • Efficient analytic frequencies for RI-DFT, hybrid DFT, Hartree-Fock and MP2 (also featuring QM/MM Hessians, ECPs, DKH/ZORA, van der Waals corrections etc., COSX and RI approximations).
  • Interface to the large-scale DMRG program "BLOCK" developed by Garnet Chan and co-workers. it can be used together with the CASSCF module of ORCA.
  • The "HF-3c" method by Grimme and co-workers is a slightly parametrized Hartree-Fock variant that can be applied to very large systems and can achieve stunning accuracy.
  • Nonlocal van der Waals corrections have been implemented by the Grimme group
  • A range of modern functionals, including M06-2X, have been implemented by the Grimme group making use of the XCFun DFT library by Ulf Ekstrom.
  • Range corrected hybrid functionals have been implemented by the Grimme group
  • Coupled cluster densities and new coupled cluster methods like orbital optimized and Brueckner coupled cluster methods.
  • EOM-CCSD excitation energies for closed-shell systems.
  • MP2 electric and magnetic response properties (but no NMR yet).
  • A fully self consistent CASSCF method with spin-orbit coupling has been developed
  • The ROCIS module features a new approach to the calculation of complicated X-ray absorption spectra that are dominated by spin-orbit and multiplet effects
  • Natural transition orbital analysis for TD-DFT excited states.
  • Effective Hamiltonian (infinite order) extraction of EPR parameters from QDPT calculations using MRCI and CASSCF/NEVPT2.
  • The RIJCOSX-SCS-MP3 method.
  • Removal of near linear dependencies in the orbital basis set.
  • Improved overlap fitted COSX approximation.
  • Geometric counterpoise correction.
  • Finite nucleus for relativistic single point calculations.
  • Finite temperature SCF calculations and correct gradients.
  • Improved picture change theory for DKH magnetic property calculations.
  • Extended correlation energy extrapolation schemes making use of of LPNO methods.
  • Interface to NBO 6.0 and AIM.



Comments

JSON Helper for Applescript

Recently there has been an increased use of JSON format for data exchange.

JSON, or JavaScript Object Notation, is a text-based open standard designed for easy human-readable data interchange. It is derived from the JavaScript scripting language for representing simple data structures and associative arrays, called objects. Despite its relationship to JavaScript, it is language-independent, with parsers available for many languages including including C, C++, C#, Java, JavaScript, Perl, Python.

JSON is built on two structures

  • A collection of name/value pairs. In various languages, this is realised as an object, record, struct, dictionary, hash table, keyed list, or associative array.
  • An ordered list of values. In most languages, this is realised as an array, vector, list, or sequence.

JSON can be used to provide the results of a calculation via a web service or it could be used to provide the results of a database search, indeed the popular database mongoDB uses JSON-style document storage. It can be regarded as less verbose alternative to XML.

I just noticed that there is now an Applescript parser for JSON,

Description. JSON Helper is an agent which allows you to do useful things with JSON (JavaScript Object Notation) directly from AppleScript. JSON Helper has no interface, and runs in the background waiting for AppleScripts to ask it to do something. JSON Helper is by far the easiest way to work with JSON in AppleScript. JSON Helper lets you convert JSON directly into AppleScript records, and convert AppleScript records and list into JSON. JSON Helper also makes it easy to parse the responses of many popular web services directly into AppleScript with convenience methods for fetching and parsing the responses from URLs.

I’ve added JSON Helper to the Applescript resources page.



Comments

Scripting Vortex and MOE

One of the new features in the latest version of MOE from Chemical Computing Group is the Listener. The MOE socket listener provides an alternative to MOE/web for executing functions remotely on a running instance of MOE.

The script will download the associated PDB structures from the rcsb Protein Data Bank, put them into a database then start the browser. It may take a few seconds to download the structure; this does rely on MOE having the right proxy settings to access the internet (use the Java console to set them). You can now transfer this to MOE and amend the display to highlight the ligand.

The MOEflexalign script takes the SMILES string of the selected row generates a 3D structure and does a one-shot flexalign between the ligand in the system in MOE, and the incoming ligand.

It is probably easier to see this in action, if it appears rather small click on the YouTube icon in the bottom right corner of the video.

Full details are here




Comments

Marvin 6.1 has been released

Marvin 6.1 has been released:   New drawing and displaying features in MarvinSketch and MarvinView
Among others drawing peptid cycles and bridges is available now, and IUPAC numbers can be displayed in MarvinSketch and MarvinView
Better images to structures conversion in Document to Structure
Optical Structure Recognition tools CLiDE and Imago can be used, in addition to OSRA
New Chinese Document to Structure feature
Chemical names in the flow of Chinese sentences are detected, without the spaces that separate words in English
Marvin for JavaScript news
Homology groups has been added Structure Checker got an integral part of Marvin Beans
Installing Marvin Beans will install the fully functional Structure Checker application

  • Structure Checker: Checker names and error messages can be localized or customized
  • Elemental Analysis: Charge is taken into account in atomic mass calculation
  • Structure Checker: “Copy as action string” option is available



Comments

Papers 3 beta

I see that the new version of the reference management application Papers is now out for beta test. Reading through the release notes this looks like it will be a major upgrade, perhaps the most significant change is the use of Dropbox for syncing between devices making it easier to get access to your references. This sounds excellent however I do know of some institutions that prohibit the use of Dropbox so I was interested to see that “other cloud based syncing services in addition to Dropbox to follow”.

In addition there is:-

  • A fresh, new user interface: the new Papers experience is simpler and more organised.
  • Navigation modes to keep your work and thoughts organised.
  • Relevant article suggestions based on the content you are reading.
  • Automatic PDF download when you import articles.
  • Better than ever metadata discovery and matching.
  • Stay connected: discover tweets and posts about the articles you are reading.
  • View and annotate supplemental files directly within Papers 3.

Papers 3 will require Mac OS X Lion and above.

There are more reference management tool here.



Comments

Scripting Vortex 14

In tutorial 4 we looked at using the command line tool sddesc from Chemical Computing Group to calculate a number of molecular descriptors and then import them into Vortex. However there a couple of issues with doing this not the least ensuring all the environment variables are set correctly. An alternative is to use MOE as a web service and access the tools using the SOAP protocol (Simple Object Access Protocol). This protocol provides a specification for exchanging structured information in the implementation of Web Services in computer networks. It relies on XML Information Set for its message format.

Full details are here...



Comments

Applescript to search un1Chem

Un1Chem is a new web resource provided by the EBI, it is a 'Unified Chemical Identifier' system, designed to assist in the rapid cross-referencing of chemical structures, and their identifiers, between databases. Currently the uniChem contains data from 19 different databases:-

Since ChemBioDraw can generate InChi Keys I thought it might be interesting to write an applescript that access this service. The InChIKey is a short, fixed-length character signature based on a hash code of the InChI string. By definition, hashing is a one-way conversion procedure and the original structure cannot be restored from the InChiKey allowing confidential searching.

Full details are here



Comments

DNActions widget

DNActions is a Mac OS X Widget that can be used to perform common actions on DNA sequences. It is useful for scientists working in genetics and can be used to obtain the complement reverse of a DNA sequence, the protein translation in all six reading frames (three in the forward strand and three in the reverse), find CpG dinucleotides and calculate the composition and the Tm (melting temperature) of a DNA molecule.



Comments

Labguru

Labguru this is a mobile app for iPad, iPhone and iPod, a complement to your Labguru account, Labguru Mobile assists you with 4 essential functions: Record images of results and link them to their specific experiment, Drill down into your lab's storage locations, Manage orders and inventory with the shopping list, Retrieve protocols on your bench to execute experiments then automatically integrate results into your Labguru account

Now added to the mobile science page.



Comments

3D Printing in chemistry

3D printing is a process of making a three-dimensional solid object of virtually any shape from a digital model and I guess it is a sign that what was a bleeding edge technology has now become mainstream when the London branch of Selfridges announce that the team at iMakr, a 3D printing workshop based in Clerkenwell in London are opening an in store studio. 3D printing uses an additive process, where successive layers of material are laid down in different shapes to slowly build up the final 3 dimensional shape.

HtH25-1

Image generously provided by Molecular Graphics Laboratory, The Scripps Research Institute

I’ve tried to pull together a collection of resources that should be useful for chemists wanting to construct 3D models.



Comments

PhySyCalc

PhySyCalc is an interesting scientific calculator that lets you do full calculations but also lets you include the units. It also includes many useful mathematical functions, as well as a number of useful physical constants. Included also are the speed of light, and the mass of the electron, proton, and neutron, all with appropriate units, atomic weights, isotope weights, and isotope abundances.

GasConstant

PhySyCalc features include:

  • Intuitive, minimal buttons in portrait display for ease and speed of use
  • Quantity units supported in all calculations
  • Calculations entered in full before evaluating
  • Use of parenthesis within your calculations
  • Full featured scientific calculator
  • Left swipe display for unlimited undo. Makes it easy to find mistakes and correct them.
  • Right swipe display for redo
  • Two finger slide on display to reduce the number of significant figures
  • Complex numbers

Now added to the Mobile Science Page.



Comments

Computational Chemistry Comparison and Benchmark Database

The Computational Chemistry Comparison and Benchmark Database (CCCBDB) has released version 16 at cccbdb.nist.gov. The CCCBDB is a collection of experimental and computed (by quantum methods)  ideal-gas thermochemistry for 1591 small molecules and atoms. The properties include enthalpy of formation, vibrational frequencies, geometries, rotational constants and dipole moments.



Comments

Choosing the app to view a file.

I mentioned in my ChemDraw for iPad review that you could open files in DropBox and I had a couple of people ask how.

With the DropBox app installed if you navigate to a file and click the icon in the top right corner you get a drop down menu asking which application to open a file with.

photo



Comments

ChemDraw and Chem3D for iPad updated

I just noticed that there are a couple of updates on my iPad, in particular ChemDraw and Chem3D for iPad have both been updated. What is particularly appealing is that they certainly seem to be listening to their users with several of the top requested features now being incorporated. I’m particularly delighted to see DropBox fully integrated as a sharing capability, for a mobile device this is absolutely critical. At the moment you can upload CDXML, PNG or PDF file formats, and you can only save to a ChemBioDraw folder within DropBox. Perhaps unsurprisingly social media outlets (Twitter and Facebook) are now also supported.

Chem3D now has the ability to pull more structures from public databases, perhaps in the next update of ChemDraw we might see the ability to pull structures from public databases such as ChemSpider?

The ability to add text boxes to structures and schemes will be very useful and will make this a more useful app for note taking. The default text seems to be Times New Roman but you can change text style using the “Colours and Styles” button. The ACS template is now available, but you can’t use your own templates.

ChemDraw for iPad 1.0.2 Features

  • Text capability to annotate structures and reactions (single-most requested feature in product reviews)
  • Adjustable arrows (another top requested item)
  • More sharing capabilities including DropBox, Twitter, Facebook, and Moxtra
  • Group Flick-to-Share (based on our summer pilots and geared toward educators)
  • Orbitals, brackets
  • Two categories of templates (structures)
  • Enhanced periodic table keyboard capabilities including an ability to quickly type a chemical formula
  • American Chemical Society template
  • Simplified Chinese language support
  • Korean language support   Chem3D 1.0.2 Features

  • More sharing options including DropBox, Twitter, Facebook and Moxtra

  • Ability to pull in more structures (PDB and CIF) from public databases including now by keyword search for structure or author
  • Group Flick-to-Share capabilities
  • Simplified 3D printing output (now via DropBox or email)
  • Simplified Chinese language support
  • Korean language support

These are excellent updates and well worth installing. A minor comment since Chem3D can import PDB structures from public databases, it might be nice to be able to save them in PDB format.

I’ve updated review I wrote.



Comments

Firefly 8.0.0 released

Firefly (previously known as the PC GAMESS) is a freely available ab initio and DFT computational chemistry program developed to offer high performance on Intel-compatible x86, AMD64, and EM64T processors. Firefly package is being developed by the Firefly Project Team.

The Mac OSX version can be downloaded here together with installation notes and user and quick start guides.

Details of this major update can be found on the news page



Comments

LeView: automatic and interactive generation of 2D diagrams for biomacromolecule/ligand interactions

The latest issue of Journal of Cheminformatics has an article describing Ligand Environment View; Journal of Cheminformatics 2013, 5:40 DOI a Java program that can be used to generate 2D representations of ligands and their environments and binding interactions from PDB entries. The application can be downloaded from here, the source code is also available.

The image below was generated from 3K83 the Crystal Structure Analysis of a Biphenyl/Oxazole/Carboxypyridine alpha-ketoheterocycle Inhibitor Bound to a Humanized Variant of Fatty Acid Amide Hydrolase.

leviewimage

It seems that whilst Hydrogen bonds are clearly defined pi-stacking interactions are not and in my brief experiments bonding to halogens was not detected 3GT3



Comments

Marvin for Javascript

The Marvin package has been updated to include Marvin for Javascript and has been released. It is a light-weight chemical editor suitable for generating standard chemical structures and simple queries on modern web browser pages without the need for installing Java. It provides all the essential features for quick and easy structure drawing as well as flexible editing options for molecular manipulations



Comments

MONA - Interactive manipulation of molecule collections

Manipulating large collections of molecules can be a laborious exercise, involving many repetitive tasks such as s checking for duplicates or filtering by physico-chemical properties as you sift through vendors catalogues. A recent publication Journal of Cheminformatics 2013, 5:38 DOI describes a tool that may be useful.

To support intuition-driven processing of compound collections, we developed MONA, an interactive tool that has been designed to prepare and visualize large small-molecule datasets. Using an SQL database common cheminformatics tasks such as analysis and filtering can be performed interactively with various methods for visual support. Great care was taken in creating a simple, intuitive user interface which can be instantly used without any setup steps. MONA combines the interactivity of molecule database systems with the simplicity of pipelining tools, thus enabling the case-to-case application of chemistry expert knowledge.

Mona has been built on top of the well-known Naomi cheminformatics framework that has been proven to be robust, accurate and extremely efficient. Mona facilitates:

  • Loading molecules files stored in SDF, MOL2 or SMILES-format
  • Scanning entire directories for molecule data
  • 2D depiction of hundreds of thousands of molecules
  • Duplicate removal
  • Filtering based on physic-chemical properties, functional groups, and substructures
  • SMARTSediting and SMARTSmatch-visualization
  • Set-operations such as union, intersection, sub-set splitting
  • Visualization of property distributions

mona

There are more details on the website http://www.zbh.uni-hamburg.de/mona and the Mac OSX version is being distributed by BiosolveIT here.



Comments

Expanding Computational Chemistry with GPUs

I see there is a session on GPU enabled science at the September ACS meeting.

Link to Abstracts.

A day and half of talks in the Division of Computers in Chemistry

NVIDIA will also host poster competition for GPU accelerated computational chemistry on Sept. 10th evening. NVIDIA will award a free GPU to the author of best poster selected by a panel of experts.

There is a listing of GPU-accelerated scientific applications here.



Comments

Crunchyard

Can't afford your own super computer ? I’ve just been sent details of CrunchYard this service allows scientists and engineers to submit simulations and run them on CrunchYard's system through an easy to use web interface. By making use of CrunchYard's cluster it means you don't have to buy and manage your own equipment. A brief look suggests there are a range of Computational Chemistry applications.

CP2K
LAMMPS
GAMESS
GROMACS

When you register you get 20 credits free which should be enough to test things out, further credits can then be purchased. For most applications one credit seems to get you 1 CPU for an hour. The FAQ section also provides access to demonstration input files for each of the packages.

computer cluster



Comments

fmcsR: Mismatch Tolerant Maximum Common Substructure Searching in R

I’m not a big user of R a free software environment for statistical computing and graphics, but occasionally I notice cheminformatics modules being published. The latest issue of Bioinformatics DOI has a paper describing “fmcsR: Mismatch Tolerant Maximum Common Substructure Searching in R”.

The fmcsR package provides an R interface, with the time consuming steps of the FMCS algorithm implemented in C++. It includes utilities for pairwise compound comparisons, structure similarity searching, clustering and visualization of MCSs. In comparison to an existing MCS tool, fmcsR shows better time performance over a wide range of compound sizes. When mismatching of atoms or bonds is turned on, the compute times increase as expected, and the resulting FMCSs are often R1C5 substantially larger than their strict MCS counterparts. Based on R1C6 extensive virtual screening (VS) tests, the flexible matching feature enhances the enrichment of active structures at the top of MCS-based similarity search results. With respect to overall and early enrichment performance, FMCS outperforms most of the seven other VS methods considered in these tests.

fmcsR is freely available for all common operating systems from the Bioconductor site http://www.bioconductor.org/packages/devel/bioc/html/fmcsR.html.



Comments

QUACPAC v1.6 released

OpenEye have announced the release of QUACPAC v1.6. This release incorporates several improvements and some bug fixes.

The chemistry of molecular interactions is a matter of shape and electrostatics, but doing electrostatics poorly is worse than doing none at all; accurate charges are required. Even the best charge models are useless if protonation states are wrong. QUACPAC attempts to offer everything necessary to do charges correctly. It includes pKa and tautomer enumeration in order to get correct protonation states, partial charges using multiple models that cover a range of speed and accuracy, and electrostatic potential map construction and storage

Updated

  • molcharge now uses the -method parameter for selecting a charge model. All individual flags for charge models have been removed.
  • tautomers will now allow interconversion of [NH2+]= and [NH3+]-.
  • tautomers now has a -warts option. Enabling this options will number the output molecules with an @ symbol.
  • The default AM1BCC charge model in molcharge now lightly restrains the AM1 geometry optimization to the starting coordinates. This allows the important relaxation of bond and angle degrees of freedom while greatly reducing the potential to alter the molecule’s conformation away from its starting coordinates.
  • The AM1BCC charge models -method am1bccsym and -method am1bccspt in molcharge now symmetrize the partial charges over bond-topologically equivalent atoms, e.g. methyl hydrogens, in keeping with the original model. This is especially important with conformationally flexible molecules.
  • molcharge now has a .fail file to output molecules that do not charge correctly.
  • fixpka has been refined to reflect feedback from collaborators. In particular isoxazoles and oxadiazoles were added while pyrazoles and aryl sulfonamides were refined. Aryl sulfonamide refinement also incorporated changes based on newly obtained experimental data.



Comments

iNMR Offers

I see the developer of iNMR has a number of opportunities to win copies of the excellent iNMR.

Details are here.

As we come up to the start of a new academic year there are also a couple of student promotions.

http://www.inmr.net/fall.html

http://www.inmr.net/annual.html

fig_01

There are more spectroscopy applications here.



Comments

Overview of SCM tools

It is sometimes difficult to keep the website up to date with some of the software that I don’t use and so I was delighted when Fedor Goumans contacted me to highlight some of the updates at Scientific Computing and Modelling. While ADF is still SCM's most widely used program, SCM offers a comprehensive modelling suite consisting of several different tools.

IRspectrumFerrocene

I have written a brief overview here.

Here is a list of the reviews available.



Comments

Installing Decoy Finder under Mac OS X

DecoyFinder is a graphical tool which helps finding sets of decoy molecules for a given group of active ligands. It does so by finding molecules which have a similar number of rotational bonds, hydrogen bond acceptors, hydrogen bond donors, logP value and molecular weight, but are chemically different, which is defined by a maximum Tanimoto value threshold between active ligand and decoy molecule MACCS fingerprints. Optionally, a maximum Tanimoto value threshold can be set between decoys in order to assure chemical diversity in the decoy set.

decoyfinder

Having spent the weekend getting it to run under Mac OS X I thought I’d write it all up so others can hopefully do it a little more smoothly.

Installing Decoy Finder under Mac OS X



Comments

AFITT v2.3 has been released

AFITT v2.3 has been released

AFITT merges OpenEye’s Shape and MMFF technologies into a new combined forcefield that fits small molecules into crystallographic density while maintaining excellent chemistry. The AFITT GUI also provides an interface to external refinement programs and tools to validate the refinement including interactive Ramachandran plots and real-space correlation coefficient calculation.

ENHANCEMENTS:

  • PM3/AM1 semi-empirical quantum force field support
  • Better density detection, especially for poor ligand density
  • Optimization enhancements for high-strain ligands
  • (AFITT-GUI) – Protein side-chain fitting (not enabled by default)
  • (AFITT-GUI) – Hydrogen bond visualization (on by default)
  • (AFITT-GUI) – Conflicts with default dictionaries (CCP4) visualized
  • (AFITT-GUI) – Speed improvements in wizard navigation
  • (AFITT-CL) – More control on report and logging generation



Comments

VHELIBS, a validation helper for ligands and binding sites

The Validation HElper for LIgands and Binding Sites (VHELIBS) is software that aims to ease the validation of binding site and ligand coordinates for non-crystallographers. It is written in java and can be downloaded from github here. I have not tested it extensivey but on my cursory look it seems to work fine under Mac OS X, provided you have installed java.

Using a convenient graphical user interface, it allows one to check how ligand and binding site coordinates fit to the electron density map. VHELIBS can use models from either the PDB or the PDB_REDO databank of re-refined and re-built crystallographic models. The user can specify threshold values for a series of properties related to the fit of coordinates to electron density (Real Space R, Real Space Correlation Coefficient and average occupancy are used by default). VHELIBS will automatically classify residues and ligands as Good, Dubious or Bad based on the specified limits. The user is also able to visually check the quality of the fit of residues and ligands to the electron density map and reclassify them if needed.

To start the application simply double-click on the icon, and then enter a PDB code (or you can load a list from a file) the analysis takes a few mins so if you are planning to examine a list of structures you may want to set it running overnight. The results can then be examined in the viewer which is uses JMOL.

vhelibs

It all seems pretty intuitive. In the view above the ligand atoms are purple and the associated electron density red, the protein atoms are white and a dubious area of associated electron density is shown in yellow.

You can read more details here Journal of Cheminformatics 2013, 5:36 doi.



Comments

SZMAP Updated

SZMAP uses semi-continuum Poisson-Boltzmann electrostatics to map variations in solvent properties in a protein binding site. It identifies key waters, shows their interactions, compares them to the corresponding ligand atoms, and determines whether neighboring waters aid or hinder binding.

  • Multiprocessor Support : Calculations can be performed much faster with szmap and gameplan by using multiple processor on a single machine and on different machines with the same operating system installed. Because of this and other improvements to the software, numerical results will differ slightly from those produced by previous versions and the set of points that are determined to be clashing may vary slightly. szmap is highly parallelizable—big calculations scale very well when run on large numbers of processors.
  • szmapgrid will now split out all szmap grids into separate files in one step when the options -outputall_format and -prefix are used.
  • szmap_report now supports a -resolution option to control the quality of the property maps.
  • gameplan now indicates the stabilization magnitude in the log.
  • To streamline the szmap program, the following obscure command line options have been eliminated: -onlyprotein, skipmodified, -proteincharge, -proteinhydrogen, -ligandcharge, -ligandhydrogen, -chargedmol, -noprobedata, -requireexplicit, -addneutral, -addvacuum, -details. There are more direct ways to perform each of the functions that they controlled. The simple help for options in each of the SZMAP applications and utilities has been streamlined.
  • The WaterColor VIDA Extension has been updated so that it no longer changes the scale of gameplan results in VIDA.
  • The Quick Start chapter is now called the Tutorial and has been reorganized to improve clarity.

Full details are here



Comments

Script Debugger Updated

If you are looking for an alternative to Script Editor then Script Debugger might be worth a look, and it has just been updated.

Script Debugger 5.0.6 is a free maintenance release addressing a series of issues that came to light following the release of Script Debugger 5.0. This maintenance release makes Script Debugger fully compatible with Mountain Lion (Mac OS X 10.8.2) and addresses a number of stability and performance issues.

There are more useful tools on the Applescript Resources page.



Comments

SYBYL-X 2.1 released

The latest update to SYBYL-X has been released, version 2.1 is only supported on 64-bit systems. In addition Python 2.4 is no longer supported, if you are using the latest Mac OS X then you should have Python 2.5.1. To check simply type python in a Terminal window.

chrismacbookpro:~ chris$ python
Python 2.5.1 (r251:54863, Nov 13 2007, 11:10:08) 
[GCC 4.0.1 (Apple Inc. build 5465)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>>

The major changes in SYBYL_X are a New Job Control System which replaces Netbatch, giving a consistent interface that is implemented across all of SYBYL-X modules. This is compatible with popular job queuing systems like Oracle Grid Engine, LSF, and Torque, and provides improved multi-processor support for key applications (Surflex-Sim, Surflex-Dock, Topomer Search, and UNITY).

There have also been updates to the Molecular Data Explorer (MDE) including:

  • Set 3D Viewer preferences for the display of proteins
  • Switch the structure viewing between the 3D Viewer and SYBYL’s main graphics window
  • Mark compounds in the 3D Viewer
  • Mark compounds in the Grid Viewer
  • Use a right-click menu in the Grid Viewer
  • Display a regression line and or unity line in a Scatter Plot
  • Tile Viewers in a grid
  • Set precision of column data
  • Save structures to a database
  • Export structures and associated column data to a MOL2 file
  • Copy a table

The Python QSAR functionality is now accessible outside of SYBYL as standalone Python scripts. Results of the Python jobs can be read into SYBYL using the new readXML expression generator. See $TA_LIB/python/lib/python2.7/site- packages/tripos/qsarutl/README for more information.

QSAR Project Manager enhancements include the ability to:

  • Modify names of structure sets and descriptor sets via a right-click menu
  • Rename and delete items in the Project Data list via a right-click menu



Comments

MOPAC speed improvements

The research group headed by Prof. Dr. Gerd B. Rocha at the Federal University of Paraiba, Brazil, has been successful in implementing a significant speedup. Two modifications have been made: many of the old, slower, operations have been replaced by the Intel Math Kernel Library, and sections of the code have been parallelized to take advantage of multi-threading. Details of the modifications can be found here

Times, in seconds, for a single-point calculation run on a 2 x 2.93 GHz 6-Core Intel Xeon with 16Gb of 1333 DDR3 memory chips Mac Pro computer, using 12 of the 24 threads

Species #atoms Current MOPAC2012 MOPAC 2012 with MKL MOPAC 2012 with MKL and multi-threading
Naphthalene 18 0.02 0.15 0.02
(H2O)573 1719 3,082.23 584.78 79.3
1G6X 1455 8,612.57 1,240.48 142.07
1RNB (Barnase) 2066 34,372.13 4,108.87 411.26


The improved MOPAC is available and can be downloaded from  http://openmopac.net/

In MOPAC, proteins can be modeled using the MOZYME technique, however, that technique is limited to closed shell RHF calculations. This means that proteins with free radical sites, excited state proteins, and proteins containing iron, chromium or other transition metal atoms should not be modeled using MOZYME. The new MOPAC reduces the computation time so that conventional MOPAC methods can now be used for many proteins. This means that it is now practical to use conventional MOPAC methods - RHF-CI and UHF - for modeling most of the smallerproteins, and by implication that it will be possible to model many systems that currently cannot or should not be modeled using MOZYME.



Comments

Multiwfn added to alphabetical listing

Multiwfn is capable of plotting curve map, plot plane map, generate grid data and display isosurface, perform topology analysis and basin analysis for ELF (electron localization function), as well as ELF-pi, ELF-sigma and localized orbital locator (LOL).


Comments

eFindSite now available for MacOS X

eFindSite is a ligand binding site prediction and virtual screening algorithm that detects common ligand binding sites in a set of evolutionarily related proteins and is described in detail in a recent publication. Brylinski M, Feinstein WP.  2013.  eFindSite: Improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands. J Comput Aided Mol Des. 27(6):551-567 DOI It employs a collection of effective algorithms, including highly sensitive meta-threading approaches, improved clustering techniques, advanced machine learning methods and reliable confidence estimation systems.

fig

eFindSite is available as a webserver and a standalone software distribution, and as of yesterday it is now available for Mac OS X!

UPDATE

A reader sent in detailed instructions for installation

  • OS X has perl already installed (with XCode/Command Line Tools I think)
  • Install perl cpanm module:

    sudo cpan App::cpanminus

  • type yes for automatic configuration

  • Install other perl modules:

    sudo cpan File::Temp sudo cpan File::Slurp

  • zlib should already be installed

  • Download gzstream: http://www.cs.unc.edu/Research/compgeom/gzstream/gzstream.tgz
  • Build gzstream:

    cd ~/Downloads/gzstream/ make

  • I couldn't manage to download f2c from the link provided - ftp.netlib.org seems to be down? (Should be www.netlib.org/f2c )

  • Found a mirror: http://netlib.sandia.gov/cgi-bin/netlib/netlibfiles.tar?filename=netlib/f2c
  • Download, untar, then also unzip libf2c.zip inside the f2c directory.

    cd ~/Downloads/f2c/libf2c/ make f2c.h -f makefile.u make -f makefile.u

  • Download libsvm: http://www.csie.ntu.edu.tw/~cjlin/cgi-bin/libsvm.cgi?+http://www.csie.ntu.edu.tw/~cjlin/libsvm+tar.gz

  • Build libsvm:

    cd ~/Downloads/libsvm-3.17/ make ar cr libsvm.a svm.o

  • Download eFindSite: http://brylinski.cct.lsu.edu/content/efindsite-standalone-package

  • Untar it. We then need to copy the dependencies into the lib directory:

    cp ~/Downloads/gzstream/gzstream.h ~/Downloads/efindsite-1.1/lib/gzstream.h cp ~/Downloads/gzstream/libgzstream.a ~/Downloads/efindsite-1.1/lib/libgzstream.a cp ~/Downloads/f2c/libf2c/f2c.h ~/Downloads/efindsite-1.1/lib/f2c.h cp ~/Downloads/f2c/libf2c/libf2c.a ~/Downloads/efindsite-1.1/lib/libf2c.a cp ~/Downloads/libsvm-3.17/svm.h ~/Downloads/efindsite-1.1/lib/svm.h cp ~/Downloads/libsvm-3.17/libsvm.a ~/Downloads/efindsite-1.1/lib/libsvm.a

  • gcc 4.4 is required to properly compile eFindSite (Xcode has 4.2.1 I think)

  • install MacPorts: http://www.macports.org/

  • update software repos:

    sudo port selfupdate sudo port install gcc44

  • in eFindSite Makefile (~/Downloads/efindsite-1.1/src/Makefile) change "CXX = g++" to "CXX = g++-mp-4.4"

  • Then build it:

    cd ~/Downloads/efindsite-1.1/src/ make



Comments

MacMolPlt 7.5 has been released

MacMolPlt 7.5 has been released

This version includes the following changes: 

  • Added support for H and I basis functions.
  • Fixed a crash under windows related to prototype selection with a single atom.
  • Fixed issue on OSX preventing quit from the dock icon from working.
  • Fixed a couple of cases where a 2D surface was not updated appropriately.
  • New splash screen - guess the orbital!

Binaries and source files are available here



Comments

IQmol updated

The free open-source molecular editor and visualization package IQmol has recently been updated to include

  • Revamped molecular builder:
  • Add atoms, functional groups, EFPs and entire molecules
  • Extensive and extensible library of molecules and fragments
  • OpenGL shader support:
  • Allows greater configurablity of appearance
  • Users can add their own shaders.
  • ESP plotting from a Distributed Multipole Analysis (from Q-Chem output file)
  • Animation of molecular surfaces
  • SGE queue system support for remote submission

ss5_small

IQmol now has its own Youtube channel which contains some animations generated with IQmol.



Comments

ACEMD webinar

The number of scientific application making use of graphics card processing continues to increase and NVIDIA are hosting another webinar. The latest webinar describes the use of ACEMD.

ACEMD is a production bio-molecular dynamics software specially optimized to run on graphics processing units (GPUs) on graphics cards. It reads CHARMM/NAMD and AMBER input files with a simple and powerful configuration interface. ACEMD allows performance equivalent to over 100 CPUs and microsecond long trajectories on workstation hardware. ACEMD is the computational engine behind one of the largest distributed computing project worldwide GPUGRID.net nowadays summing thousands of GPUs. ACEMD is compatible with CUDA and OpenCL, the new standard framework for parallel and high-performance computing over different architectures.

You can now view previously recorded webinars on GPU accelerated applications such as AMBER, NAMD, GROMACS and FastROCS here free registration required. There is a page of GPU-accelerated scientific applications here



Comments

Plugins for Open Babel

I’ve just read a new blog entry on Noel O’Blog regarding the development of useful cheminformatics code, in the piece he advocates the use of Open Babel

I'm going to propose that you should write or adapt this code as an Open Babel plugin. I've just done this for Confab, the conformer generator I wrote some time back. If you do this, you don't need to consider how to put together the build infrastructure, write the code for reading/writing file formats, or for handling command-line options and arguments (in fact, you get a lot of additional functionality for free). More generally, the software will compile cross-platform, be included in every major Linux distribution and be available to a very large number of people. It will also have a lifetime beyond the end of the grant that funded it.

I couldn’t agree more, added to which it is nice to see how the code you contribute can be built on and extended.



Comments

Dotmatics User Group Meeting

As you may have noticed I’ve written a variety of scripts for Vortex in the Tutorials section, if you would like to find out more about this and the other software packages available it might be worth you attending the free Dotmatics User Group Meeting.

http://www.dotmatics.com/ugm-registration/

The software has been coming on very impressively and this is the ideal opportunity to see what it is now capable of delivering.

Update As an aside I've been told that if you answer the question "How did you hear about the UGM?" with "Chris told me there was cake" there might be a nice surprise ;-)



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Insights for data analysis

Insights is a self-organising data modelling tool that is particularly useful for noisy or fuzzy data.

som_3

Insights makes optimal use of the 64-bit processing power of your machine utilising all available cores in modern desktop machines.

speedup_2

The cost is $80-$2000 depending on the version, and there is an education discount and a free trial. There also currently appears to be a discount code.

There is a comprehensive list of data analysis tools for Mac OS X here.



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QMForge 2.2 released

QMForge is a program used to analyze the results of quantum chemistry (DFT) calculations. Gaussian 98/03, ADF, GAMESS (US), GAMESS (UK), PC-GAMESS, Jaguar, and ORCA files are supported (see below). The following analyses are available:

  • Mulliken Population Analysis (MPA)
  • C-squared Population Analysis (SCPA)
  • Löwdin Population Alanlysis (LPA)
  • Overlap Population Analysis (OPA)
  • Mayer's Bond Orders
  • Charge Decomposition Analysis (CDA)
  • Fragment Analysis

MPA, CSPA, LPA, and OPA require a user-defined set of fragments, and prints the percent contributions those fragments make towards each molecular orbital in the molecule. Mayer's bond orders calculates the bond orders between each pair of atoms in the molecule. CDA and Fragment Analysis require three or more calculations (one for the entire molecule, and two fragment calculations), and provide information about the bonding interactions between fragments.

optimization-mac



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Regress+ v2.7 released

Regress+ v2.7 has been released
Univariate Data Modeling: Equations and Distributions

  • Plain textfile input
  • Equations, with or without uncertainties (weights)
  • Distributions, continuous or discrete data
  • Discrete data grouped or ungrouped
  • Datasets up to 4,294,967,295 points (minimum 7)
  • Up to 10 parameters
  • User-selected optimization criterion (where appropriate)
  • Least squares
  • Minimum average abs(residual)
  • Maximum likelihood
  • Minimum K-S statistic
  • Minimum chi-square statistic
  • Full, dated Report (textfile)
  • Robust goodness-of-fit testing for distributions
  • Tunable precision
  • [Optional] State-of-the-art (BCa) central confidence intervals (90, 95 and 99 percent)
  • Tunable precision
  • High-quality (PDF, PNG) plots with one keystroke!
  • X/Y plot, with or without error bars
  • PDF plot
  • CDF plot
  • Probability plot for goodness-of-fit (see above)
  • [Optional] Logarithmic axes (when appropriate)
  • Editable axis labels
  • Automatic tick marks/labels (see above)
  • [Optional] Predictions for unobserved values or percentiles
  • With confidence intervals if desired
  • [Optional] Constant parameter(s)
  • 21 Built-in Equations
  • Plus user-defined model
  • [Optional] Test residuals for systematic error
  • [Optional] List data with fitted estimates and residuals
  • [Optional] Simulated-annealing mode for initial parameter estimates
  • 59 Built-in Distributions
  • 9 continuous, symmetric
  • 27 continuous, skewed
  • 11 continuous mixtures
  • 6 discrete
  • 6 discrete mixtures
  • [Optional] Creation of synthetic samples
  • No hidden assumptions anywhere
  • No approximations, apart from those common to sampling and bootstrapping generally
  • No data transformations of any kind
  • Extensive documentation
  • Data Modeling with Regress+ (PDF, 100 pages, 43 figures, 14 tables)
  • Compendium of Common Probability Distributions (PDF, 136 pages, 59 figures, also published separately)
  • Sample input and output files
  • Completely free! No cost, no license, no registration.

There is a list of data analysis tools here.



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Mobile Science Page Updated

I’ve updated the mobile science page adding a few new applications.

3D Molecules Edit&Drill is designed to enable students to build, construct, modify and examine molecules in 3D.

CueMol viewer for iOS is an interactive macromolecular viewer for structural biologists. CueMol viewer allows the users to open and view the scene files made by the desktop version of CueMol, and the Protein Data Bank (PDB) format files, as well.

GLmol Free and open source 3D molecular viewer based on WebGL and Javascript. GLmol runs on newer versions of Firefox, Chrome, Safari or Opera. Internet Explorer is not supported. GLmol also runs on WebGL enabled safari in iOS.

iPharosDreams is a molecular visualization app for iPad that allows you to perform in-silico drug discovery. This app basically has functions that download protein structure files from Protein Data Bank, display 3D molecules, touch, rotation, zoom in/out. Hierarchy structure of molecules is shown with a table that select precisely components in a protein and related things. Above all, you can generate pharmacophores and analyze 3D protein-ligand interaction of biological macromolecules for in-silico drug discovery. You can select a ligand from a protein and generate a binding site from the selected ligand. From the binding site, also you can generate receptor based pharmacophores and get inspiration for good hit compounds interact with the protein well.

Many thanks to those who suggested links.



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Platypus Updated

Platypus is a developer tool for the Mac OS X operating system. It creates native Mac OS X applications from interpreted scripts such as Applescript or shell scripts, or Perl, Ruby and Python programs. This is done by wrapping the script in an application bundle along with a native executable binary that runs the script.

The update includes

  • New "Prompt for file on launch" option
  • Redesigned Drop Settings sheet
  • Fixed issue where version would not appear in Get Info in Finder (missing CFBundleShortVersionString)
  • Generated apps have NSHumanReadableCopyright defined again
  • Extensive updates to documentation
  • "Provide as a Mac OS X Service" no longer enabled by default
  • Removed all support for file types. They are ancient crust now mostly ignored by Mac OS X and should no longer be used.
  • Improved uninstall script
  • Fixed issue where a generated icon file referenced in a Profile could be overwritten
  • Documentation files now open in default browser, not in default .html handling app
  • Fixed broken nib optimization. Platypus now correctly detects XCode 4 installs.

There are a number of other tools on the Applescript resources page.



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ProDy

ProDy is a free and open-source Python package for protein structural dynamics analysis. It is designed as a flexible and responsive API suitable for interactive usage and application development.

Structure analysis

ProDy has fast and flexible PDB and DCD file parsers, and powerful and customizable atom selections for contact identification, structure comparisons, and rapid implementation of new methods.

Dynamics analysis

  • Principal component analysis can be performed for heterogeneous X-ray structures (missing residues, mutations) mixed structural datasets from Blast search NMR models and MD snapshots (essential dynamics analysis)
  • Normal mode analysis can be performed using Anisotropic network model (ANM) Gaussian network model (GNM) ANM/GNM with distance and property dependent force constants

Bakan A, Meireles LM, Bahar I ProDy: Protein Dynamics Inferred from Theory and Experiments 2011 Bioinformatics 27(11):1575-1577 DOI



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Pubchase Updated

PubChase is a science literature search and recommendation tool, available online and on your mobile device. It has recently been updated to include cloud-synced PDF support, making PubChase truly mobile. Users can now add/delete library PDFs on the web and iPad, with ability to view the PDFs on the iPhone as well.

They have rolled out a social network component on PubChase. This allows users to subscribe to libraries of others and to see a feed of recently-added papers by those in their network. Offering automated personal recommendations and social-based literature discovery.

They have also launched a backstage-stories series to add a personal layer to published research. This and next month, they are publishing a story per week, by invitation. However, after it is established they will open the posting to the authors themselves, thus creating an article-centered tumblr for scientists. (The first essay was http:www.pubchase.com/essay/my-break-up-nature-paper-by-meleah-a-hickman-4) An interesting idea and well worth a look.



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Teaching chemistry Apps

I was recently sent a link to an educational chemistry app Chemistry By Design: Learning by Using the Graphical Language of Organic Chemistry by University of Arizona. I had a quick look at it and it seems quite an interesting way to learn organic synthesis. There around a thousand synthetic routes to explore and it seems to cover a wide range of synthetic organic chemistry, the synthetic targets include natural products and pharmaceuticals. I was particularly delighted to see that Woodward’s 1954 synthesis of strychnine is included.

photo

Whilst looking it up I noticed several other educational chemistry apps, Organic Chemistry Essentials, Organic Chemistry FlashCards. What is clear is it would be very useful to have a science category to help find these sort of applications.

There is a list of mobile science apps here.



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ChemSpider and spectral information

There was an interesting entry on the ChemSpider blog this week, apparently they are starting to capture spectral information

The RSC now encourages authors for several of our journals to supply extra information, structures and spectra in their original file formats – which are attached to the article as supplementary information. Already we’ve seen several submissions of data that we have incorporated into ChemSpider records, both enriching the ChemSpider database and also showcasing the research of these authors through their publications. In this way, the RSC hopes to encourage the addition of reusable data files to the research paper as the start of its efforts to promote increased data sharing within chemical science research. In a few short weeks we’ve received a number of submissions from authors that include key chemical structures as mol files and in some cases extra data including 1H and 13C NMR spectra as well as UV and IR spectra.

As you can see from this entry ChemSpider ID: 28945607 there are spectra associated with this record. unfortunately at the moment you can’t view them in Safari because the javascript looks for Internet Explorer and Firefox. Fortunately you can get around this by changing the user agent from the “Develop” menu in Safari.

temp1

Once you have done that you can see the spectra displayed using a Java applet.

chemspiderSpec



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Marvin Update

New features and improvements
Image I/O
The following file extensions were removed from the "Files of Type" list on the Import Image dialog: *.ps, *.pdf, and "All Files".
PDF files can be imported through the "File > Open" menu.
Calculation Services
SOAP version 1.2 webservices are supported.

There are a number of bug fixes.

On the Mac clipboard handling has been improved, On Mac OS X, copy-paste (from MarvinSketch to, e.g., TextEdit) did not transfer the atom colors.



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Wizard 1.3.6 released

Wizard 1.3.6 is a minor bug-fix and feature release now available in the Mac App Store.

Here's the list of changes:

  • Support for batch-importing multiple files of the same type
  • New: Count Distinct Values function in the Pivot view
  • Fix minor issues with importing from XLS files
  • Pro only: Support for importing .dta files created with Stata 13

There is a list of data analysis tools here



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Applescript Update

There have been a number of discussions about the impact of sandboxing on Appelscript, the latest update (10.8) helps to clarify the situation.

The full release notes are here.

Sandboxing and Running Scripts

Sandboxing your application may require changes to how it runs scripts. The usual method in the past has been NSAppleScript, but since scripts typically rely on sending Apple events and the default sandbox profile does not allow sending Apple events to any other application, this often does not work correctly when in a sandbox. Scripts run from your application will fall into one of three categories: • Self-targeted scripts. Your scripts only send events to your application and never to any other application. Continue to use NSAppleScript as before. • Built-in scripts. Your scripts are built as part of your application, and will not change after shipping. Continue to use NSAppleScript, but add entitlements for sending events to the target applications. • User scripts. Your scripts are supplied by the end user, and may use any other application. Use NSUserScriptTask. The scripts must be stored in a special location (use NSApplicationScriptsDirectory to determine where), and will run outside of your sandbox.

Sandboxing and Scriptability

Sandbox policy does not restrict receiving of Apple events, so in general, your application’s scriptability code will not be affected by sandboxing. Note: As mentioned under Compatibility above, sandboxed applications will not be able to access files referred to in commands using a string path. Any parameters or properties in your application that refer to files should be declared as type file, and not type text. Apple Event Manager will add sandbox extensions to events that have file-like parameters, but only if the parameter is of a recognized file-like type: typeAlias, typeFileURL, cFile, and so on. Without these extensions, the file will not be accessible from the target application’s sandbox, and the command will probably fail.

Your application’s scripting definition (sdef), however, should be updated to add access groups: groups of commands, classes, and so on that a sandboxed client can request to use with the new com.apple.security.scripting-targets entitlement. For example, Mail defines a “compose” access group that allows creation and editing of an outgoing message, but nothing else. This is safer than the old com.apple.security.temporary-exception.apple-events entitlement, which allows access to the entire scripting interface. See sdef for details of the markup format.



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S-Lab Award

The Paterson Institute for Cancer Research were the winners of The Laboratory Information Technology Award at S-Lab. They make extensive use of the cross-platform Dotmatics products.

You can read more here.



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Strip-it version 1.0.2 has been released

Silicos-it have just announced that Strip-it version 1.0.2 has been released and is now available for download. Strip-it 1.0.2 includes a new command line feature, the --noHeader option, to suppress the generation of the header line in the output. This new release is based on a patch kindly provided by Bjrn Grning from the University of Freiburg.



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BlazeGPU

I was at the Cresset UGM last week and had a chance to hear more about BlazeGPU. The original CPU application Blaze uses the shape and electrostatic character of known ligands to rapidly search large chemical collections for molecules with similar properties. The latest version BlazeGPU runs at 40 times the speed of the CPU version of Blaze but loses nothing in accuracy. At a fraction of the hardware cost, BlazeGPU delivers the same effective, ligand based virtual screening as Blaze, based on the shape and electrostatic nature of molecules.

BlazeGPU is written in OpenCL and OpenCL libraries are available from NVidia and AMD for their graphics cards, but also from Intel for the CPU and for their new Xeon Phi coprocessor cards. BlazeGPU is currently designed only to run on the GPU - for CPU-only clusters the original code is just as fast, and on a machine with a reasonably fast GPU or two the CPU tends to run flat out just feeding data to the graphics card, so there's not that much gain running on the CPU as well as the GPU.

Currently the conformer generation still runs on the CPU, but they are looking at the possibility of porting that to OpenCL as well in the future.

The relative performance is shown in the plot below, it is worth noting that these are relatively inexpensive graphics cards that you can pick up on Amazon or ebay for a few hundred pounds. Also note for a $2.10/hour GPU instance on AmazonEC2 you can process 2m conformations.

BlazeGPU

There are more examples of GPU science here.



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Updates to ChemSpider

Those who follow the ChemSpider Blog may have noticed that there have been a number of enhancements to ChemSpider. Details are covered in three blog posts the first cover autocompletion and combined structure and property searches, the second covers searching the supplementary information and the final post describes combining searches and then using spectral information to identify a reaction product.



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A comparison of 6 javascript chart plotting packages

Fusion Charts have provided a very useful comparison of 6 javascriptHTML5 chart plotting libraries.

The six libraries are FusionCharts Suite XT, HighCharts, Google Chart Tools, Sencha ExtJS, Charts, Chart.js, Flot, jqPlot. I’ve used Flot a couple of times and found it a very useful lightweight library. But as they say choice is good.



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Bookends Updated

Bookends 12 has been rewritten from the ground up. It includes configurable spell checking, database journaling, integration of the built-in browser with the library window, enhanced formatting options,.

The full release notes are here

There is a page of reference management applications here



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Molegro Virtual Docker Update

An update to the Molegro Virtual Docker has been announced. It includes new data analysis tools that are now available directly from within Molegro Virtual Docker. Some of the new features include:

  • New and powerful regression features: Support Vector Machine regression and Partial Least Squares
  • Classification using either K-Nearest Neighbors or Support Vector Machine classification
  • Automated fine-tuning of regression and classification model parameters
  • Spring-Mass Maps for visualization of high-dimensional data
  • Clustering of data sets and subset selection
  • Principal Component Analysis
  • Outlier Detection



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MacPro

I was just looking at a few of the images of the internals of the new MacPro, I wonder how long it will be before someone produces a replacement transparent cover and subtle lighting for illumination. Could look pretty cool.

MacPro2



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ChemDoodle Updates

IChemLabs have announced a couple of updates

ChemDoodle Web Components 5.2.2 has been released, this is a minor update This update fixes some issues, and most notably stabilises the WebGL text system. They have updated a few of the demos to show off this feature:

2D to 3D Coordinates
MolGrabber 3D
PDB Ribbons

ChemDoodle mobile 1.4.1 is also now available from the App Store, the release notes include.

  • Support for the iPhone 5
  • IUPAC Naming
  • 3D coordinate generation and viewer
  • Added empirical formula to calculations
  • Added rotatable bond count to calculations
  • Added total electron count to calculations
  • Added vdW volume to calculations
  • Added complexity to calculations
  • Fixed slow performance issues on iPad in landscape mode
  • Fixed MolGrabber search issues
  • Fixed issue where the back button wouldn’t appear on the last help page
  • Fixed login issues
  • Performance improvements
  • General improvements and fixes



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OpenEye updates

OpenEye have announced updates to a couple of their products

OMEGA v2.5 is designed to produce high quality multi conformer databases.

Highlights from this release include: OpenMPI version 1.6 is supported on all platforms. The -mpinp and -mpihostfile flags are now used to run OMEGA and makefraglib in MPI mode. These new flags replace the oempirun script. PVM (parallel virtual machine) is no longer supported. An option has been added to allow hydrogen atoms in -OH, -SH, and amines to take part in conformational sampling. This new option can be enabled via the -sampleHydrogens parameter. By default, hydrogen atoms are not sampled. Now using -fixsmarts without -fixmol will rematch for every input structure. Previously, this would only match the first input structure and reuse that match for the rest of the calculation. Using both -fixsmarts and -fixmol will continue to match against the fixmol and use that match for the entire calculation.

EON v2.2. compares electrostatic potential maps of pre-aligned molecules and determines the Tanimoto measures for the comparison.

Highlights from this release include: OpenMPI version 1.6 is supported on all plafforms. The -mpinp and -mpihostfile flags are now used to run EON and makefraglib in MPI mode. These new flags replace the oempirun script. PVM (parallel virtual machine) is no longer supported. The default hitlist format has been changed from sdf to oeb for increased functionality and decreased filesize. The output format is adjustable with the -oformat parameter. Now SD tags are prefixed with EON_. The tags are optional with the -sdTags parameter. Additionally, any existing ROCS tags will not be removed because ROCS and EON tags no longer conflict



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UCSF Chimera Version 1.8

The latest release of UCSF Chimera has been announced. Runs on Mac OS X 10.6, 10.7, and 10.8 (Snow Leopard, Lion, Mountain Lion: Intel only) or later

New features include a REST interface, session thumbnail images, electric field line display, interactive arrow repositioning, improvements to Animation, Mac multi-touch trackpad support, and support for new formats: AutoPack results, Rich Molecular Format, Gromacs 4.6 trajectories, Amira mesh (scalar).

Full details are in the release notes.

UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated.



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Running LigPlot+ under Mac OS X

I occasionally get asked to help with non-Mac applications and recently someone inquired about LigPlot+.

LigPlot+ is a graphical front-end to the LIGPLOT and DIMPLOT programs.

  • LIGPLOT - automatically generates schematic diagrams of protein-ligand interactions for a given ligand in a PDB file.
  • DIMPLOT - plots interactions across a selected protein-protein or domain-domain interface.

Whilst this application is supported under Windows and Linux there is no official support for Mac OS X, however since the GUI LigPlot is written in java and LIGPLOT is written in C there seems to be no reason why it should not run under Mac OS X and with a couple of tweaks it seems to run fine. Full details are here

interactionplot

Added to the list of Hints and Tips



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Applescript and AppleScriptObjC

With WWDC about to open tomorrow I’ll be looking with interest to see if there any changes to Applescript and AppleScriptObjC.

I thought I’d also mention AppleScriptObjC Explored the book by Shane Stanley, this is the definitive guide to creating AppleScript Objective-C applications, and until Apple improve the documentation this is essential reading.

There is a list of Applescript resources here.



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BBEdit updated

BBEdit 10.5.4 is a focused maintenance update which includes fixes for reported issues and includes no new features.

The full release notes are here



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Mobile Science apps

I’ve already mentioned ChemDraw for iPad but Perkin Elmer also released Chem3D for iPad yesterday, it should be noted that Chem3D for iPad is a simple molecule viewer and it does not include the computational abilities of the desktop version.

Both are now included on the mobile science page



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ChemDraw for iPad

About three decades ago I stopped using a stencil and a Rotring pen to create chemical structures for publications and started using ChemDraw on a Mac, at the time it transformed the standard of structures in publications and it has continued to set the standard for publication quality chemical structures. Over the years the software has developed and moved into cheminformatics, spectroscopy and more recently biological drawing. This lead to the rebranding as ChemBioDraw but most of the chemists I know still call it “ChemDraw”. So it is perhaps not surprising that I feel rather pleased that the iPad version is entitled simply ChemDraw.

You can read a full review here.



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Schrödinger Software Release 2013-1

Schrödinger have just announced the latest release of their entire suite of software programs, this covers tools for drug design, material science, biological modelling and general purpose modelling.

There are a huge number of new features and improvements in the small molecule drug discovery suite as well as Materials Science. However a couple of features caught my eye, pKa prediction for both rule-based and QM-based methods has been improved. Covalent ligand docking has been added and includes a variety of common docking chemistries. Improved pi-stacking interactions in docking. The molecular dynamics has been updated and now includes support for GPU-acceleration. The QM tools look to have been updated and the interface improved. ADME tools have been updated and in particular P450 site of metabolism has improved accuracy.

Predictive capabilities that can be applied across a wide range of chemical systems, including ,Reaction thermochemistry and reaction path exploration ,Rate constants for reactions and transport from transition state theory ,Validated models for calculating oxidation and reduction potentials, Accurate heats of formation and atomization energies for larger systems, Reliable properties for systems containing transition metals,Efficient calculation of electric field dependent properties,Prediction of vibrational and electronic spectra for complex systems,Multiple pre-defined calculation modes representing tested simulation parameters balancing speed and accuracy.

There has also been an update to PYMOL with improved rendering speeds and a couple of bug fixes.

This is certainly a great update and well worth having a detailed look at.



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aiSee node graphing software

I’ve just added aiSee to the table of data analysis tools for MacOSX.

aiSee is node graphing software that automatically calculates a customizable layout of graphs specified in GDL (Graph De­scription Language). This layout is then displayed, and can be interactively explored, printed, and exported to various formats. There are free, academic and commercial licenses.



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R and Python

If you are planning to use R with Python for handling a large amount of data then this blog post may be of particular interest, Stepping up to Big Data with R and Python: A Mind Map of All the Packages You Will Ever Need.



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SMARTSeditor

Creating SMARTS strings can be an interesting experience, thankfully there are a few tools that make the task easier. A recent addition is SMARTSeditor from BiosolveIT, the SMARTS tools are prototypes developed by their academic partner at the Center for Bioinformatics (ZBH) of the University of Hamburg. The software may be used free of charge up until December 31th 2013.

SMARTSeditor is an interactive GUI application that lets you draw substructure patterns. Jump-starting from a molecule you may develop a SMARTS in a quite intuitive fashion by editing the topology and properties. Using pre-defined patterns for common functional groups lets you quickly reach your goal. SMARTSeditor supports recursions, allowing you to go to any level of complexity without getting lost.

smarteditor

You can read more here Schomburg, K.T., Wetzer, L., Rarey, M. Interactive design of generic chemical patterns. Drug Discov Today (2013)

You can also try the SMARTviewer out online here.



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Chemical Activity Predictor

The Chemical Activity Predictor service is the first one of the new Apps from NCI-NIH. It provides the prediction of a (growing) number of small molecule physicochemical or biological properties calculated by QSAR models created in the GUSAR software. To use it you can simply paste in a SMILES string. It is only a beta test but worth having a look at.



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mathStatica updated

mathStatica 2.7 for Mathematica 9 has just been released.

This update contains Totes amazeballs automated Plotting, Piecewise Processing Engine, another 40 univariate distributions to the built-in palettes, mathStatica 2.7’s parallel processing engine unleashes the power of your computer — automatically — featuring phenomenal speed and power for users with multi-processor machines. There are also a number of new functions, and the pallets have been updated.

There is a page of data analysis packages here.



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ChemAxon Update

ChemAxon have announced an update to their desktop suite of applications.

Version 6 for scientists:

  • All GUIs are refreshed to simplify both the user experience and access to key chemistry functions
  • Marvin for JavaScript – new light-weight chemical editor for web pages which does not require Java
  • Plexus – new web-based application for medicinal and computational chemists, featuring dynamic data visualization,

MacOSX 10.8 users should also note this support message

Many of you have bumped into the problem when the Gatekeeper Security of OS X Mountain Lion blocks launching applications downloaded not from the Apple store. The solution is to modify the default settings of the Gatekeeper:

  • Select 'Apple > System Preferences > Security & Privacy '
  • In the 'General' section the setting of ' Allow applications downloaded from :' should be set to ' Anywhere'! After this you would not get the "damaged dmg" popup and you can install the downloaded dmg. You even don't need to re-download it, the "damaged dmg" is misleading.




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ChemmineR updated

ChemmineR a cheminformatics package for analyzing drug-like small molecule data in R was recently updated. Its latest version contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity searching, classification and clustering of compound libraries with a wide spectrum of algorithms. In addition, it offers visualization functions for compound clustering results and chemical structures.

To install, start R and enter

source("http://bioconductor.org/biocLite.R")
biocLite("ChemmineR")



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Living Molecules Updated

The Living Molecules iOS app has been updated, this version now activates the phones flashlight to better capture the glyphs in dim conditions.

The Living Molecules app allows you to turn chemical structures into a molecular glyph, which can be used on documents like posters, manuscripts or web pages. Anyone who has the app can use the camera to capture molecular glyphs, and bring the chemical data onto their device. A molecular glyph is the chemical equivalent of a QR code.



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NWChem 6.3 released

An update to NWChem has been released with a host of new features.

NWChem 6.3 includes a new real-time, time-dependent density functional theory capability developed by Ken Lopata, EMSLs first William Wiley Distinguished Postdoctoral Fellow. This capability allows researchers to probe the ultrafast dynamical behavior of molecules and materials in response to an applied electric field.

With this release, researchers will for the first time be able to perform large scale coupled cluster with perturbative triples calculations utilizing the NVIDIA GPU technology. A highly scalable multi-reference coupled cluster capability will also be available in NWChem 6.3.

EMSL Computing greatly expanded NWChem 6.3 plane wave capability with access to a large set of density functional and pseudopotentials or effective potentials, and a more extensive suite of functionality for the projector augmented wave methodology.

Latest set of basis sets in the Basis Set Exchange have been added to the NWChem basis set library.In addition, NWChem 6.3 includes a new set of reaction path methodologies, tools for various spectroscopies including Python scripts to post-process UV/Vis and core spectra. Binaries are not yet available but the source code and instructions for compilation on a Mac are available are available. You will need Xcode and gfortran 4.6.2 from http://gcc.gnu.org/wiki/GFortranBinaries#MacOS



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JSME: a free molecule editor in JavaScript

Another javascript-based molecular editor JSME was recently described in the Journal of Cheminformatics, JSME is a port of the very popular JME java applet.

The actual molecule editing Java code of the JME editor was translated into JavaScript with help of the Google Web Toolkit compiler and a custom library that emulates a subset of the GUI features of the Java runtime environment. In this process, the editor was enhanced by additional functionalities including a substituent menu, copy/paste, drag and drop and undo/redo capabilities and an integrated help. In addition to desktop computers, the editor supports molecule editing on touch devices, including iPhone, iPad and Android phones and tablets. In analogy to JME the new editor is named JSME. This new molecule editor is compact, easy to use and easy to incorporate into web pages.



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MultiMarkdown Composer Updated

I’ve just added MultiMarkdown Composer to the list of Markdown editors, it has just had a major rewrite and includes a host of user requested new features. Full details are in the knowlegebase



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Living Molecules

The Living Molecules app allows you to turn chemical structures into a molecular glyph, which can be used on documents like posters, manuscripts or web pages. Anyone who has the app can use the camera to capture molecular glyphs, and bring the chemical data onto their device. A molecular glyph is the chemical equivalent of a QR code.

glyph

The glyph contains just enough information to establish a source and identification for the data, so that the content can be downloaded from the internet and viewed:

livingmolecules

I’ve been trying this out over the weekend and whilst it works, it looks like it is very resource intensive and my old iPhone 4 really struggled. This looks like an interesting project and it will be interesting to see how it develops.

I’ve added it to the list of mobile science applications.



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A couple of updates

The point and click data analysis tool Wizard Pro has been updated. In particular this update address a couple of issues

  • Preserve filter selections when switching between tables
  • Correctly parse numbers surrounded by spaces in CSV files 
  • Fix a bug where a blank header cell in an Excel spreadsheet caused subsequent columns not to be imported 
  • Fix some issues with PDF export of model images
  • Fix a crash when stacking tables with indicator variables

The Reference Management package Bookends has also been updated,

  • Get DOI was updated to deal with changes made by CrossRef
  • This includes dealing with changes made in the way CrossRef encodes accented characters.
  • Updated Import From Existing Bibliography to deal with changes made by CrossRef
  • Updated Bookends browser to detect DOIs on the Google Scholar web site to deal with changes made by Google



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Indexing the internet in a chemically intelligent manner

Some time ago I described a Safari extension that uses the chemicalize.org to index a web page for chemical content.

For an example of a “chemicalized” page have a look at this

As you can see below all molecules mentioned in the page become links that on a mouse over reveal the structure, they also provide a handy ribbon of structures across the top of the page that is useful for quickly scanning and navigation.

screnn1

A recent publication by Southan and Stracz, Extracting and connecting chemical structures from text sources using chemicalize.org. Journal of Cheminformatics 2013, 5:20 describes how this information is being used to provide better indexing of the internet in a chemically intelligent manner. They include a demonstration of a number of web pages and document sources that were indexed in this manner including PDF’s from the patent office.

chemicalize.org now has 15000 unique visitors a month – which is a huge growth compared to spring 2012. These users contribute to the database every day, making sure it’s up-to-date and contains new interests as well. The database today contains 327000 structures that were converted from 545000 names and identifiers coming from 367000 webpages.

These structures and links have now been uploaded to PubChem and if you are interested in what sort of molecules have been registered via chemicalize.org you can browse them on the PubChem website here



Comments

OSRA Updated

OSRA 2.0.0 is available for download.

OSRA (Optical Structure Recognition Application) is a utility designed to convert graphical representations of chemical structures and reactions, as they appear in journal articles, patent documents, textbooks, trade magazines etc., into SMILES or MOL files –

  • Significantly improved recognition rates. Full details of the validation are available.
  • Added recognition of Iodine, wavy bonds, etc.
  • Completely modified confidence function (values not compatible with the earlier versions).
  • Updated table detection and removal routines.
  • Created binary package for Linux (statically linked, should work on all modern Linux systems).
  • Windows and OSX versions now support multi-threading processing of PDF files.

With this release the distribution model has been changed a bit: while the source code is available free as before, to offset the development costs the installable packages for Windows, Mac OSX and Linux can be purchased for a fee.



Comments

Scripting Vortex, using OpenBabel fastsearch

One thing I’ve needed to do a couple of times recently is give an idea of how many similar compounds are available to the set of compounds I’m currently viewing. For example in designing a fragment library it is very useful to know for a particular fragment how many similar fragments are commercially available. Or when looking at the results of a high-throughput screen how many similar analogues to a particular hit were also screened.

To do this we need a way of doing a rapid similarity search of the reference database. I use OpenBabel in particular using the fast search capability with molecular fingerprints.

In Scripting Vortex 13 there is a new script to do this.

There are many more scripts and hints here.



Comments

International Workshop on OpenCL (IWOCL)

This might be of interest to those involved in developing scientific applications that take advantage of the GPU.

The International Workshop on OpenCL (IWOCL) is an annual meeting of vendors, researchers and developers to promote the evolution and advancement of the OpenCL standard. The meeting is open to anyone who is interested in contributing to, and participating in the OpenCL community. IWOCL is the premier forum for the presentation and discussion of new designs, trends, algorithms, programming models, software, tools and ideas for OpenCL. Additionally, IWOCL provides a formal channel for community feedback to OpenCL promoters and contributors.

May13-14 2013 Georgia Institute of `Technology, more detailed here.



Comments

PSI updated

PSI4 provides a wide variety of quantum chemical methods using state-of-the-art numerical methods and algorithms. PSI4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform computations with more than 2500 basis functions running serially or in parallel.Several parts of the code feature shared-memory parallelization to run efficiently on multi-core machines. An advanced parser written in Python allows the user input to have a very simple style for routine computations, but it can also automate very complex tasks with ease.

Now at Beta4 this is the first public release.

The majority of PSI4 was developed on Mac and Linux machines. In principle, it should work on any Unix system; however, we have not tested extensively on systems other than Mac and Linux. There is not a Windows version of PSI4

Psi4: An open-source ab initio electronic structure program, J. M. Turney, A. C. Simmonett, R. M. Parrish, E. G. Hohenstein, F. Evangelista, J. T. Fermann, B. J. Mintz, L. A. Burns, J. J. Wilke, M. L. Abrams, N. J. Russ, M. L. Leininger, C. L. Janssen, E. T. Seidl, W. D. Allen, H. F. Schaefer, R. A. King, E. F. Valeev, C. D. Sherrill, and T. D. Crawford, WIREs Comput. Mol. Sci. 2, 556 (2012). (doi: 10.1002/wcms.93).



Comments

R reaches version 3.0.0

R the language and environment for statistical computing and graphics has now reached version 3.0.0.

Whilst there is a list of new features and updates, those listed as most significant are shown below.

  • Packages need to be (re-)installed under this version (3.0.0) of R.
  • There is a subtle change in behaviour for numeric index values 2^31 and larger. These never used to be legitimate and so were treated as NA, sometimes with a warning. They are now legal for long vectors so there is no longer a warning, and x[2^31] <- y will now extend the vector on a 64-bit platform and give an error on a 32-bit one.
  • It is now possible for 64-bit builds to allocate amounts of memory limited only by the OS. It may be wise to use OS facilities (e.g. ulimit in a bash shell, limit in csh), to set limits on overall memory consumption of an R process, particularly in a multi-user environment. A number of packages need a limit of at least 4GB of virtual memory to load. 64-bit Windows builds of R are by default limited in memory usage to the amount of RAM installed: this limit can be changed by command-line option --max-mem-size or setting environment variable RMAXMEM_SIZE.
  • Negative numbers for colours are consistently an error: previously they were sometimes taken as transparent, sometimes mapped into the current palette and sometimes an error.

There is a list of data analysis packages for MacOSX here.



Comments

The Portable Chemist's Consultant

This is the first major scientific text that I’ve seen that specifically aims for the iPad rather than hardback books, and I suspect it will become the norm in the future. When scientific text books are so expensive, and need regular updates this becomes a very attractive model. The Portable Chemists Consultant

This is a chemistry book like no other. This is your virtual consultant. If you work in any chemical company, our aim is to make this your survival guide. This is your portable consultant, available 24/7, and offering advice that cannot be obtained by cursory use of search engines. This consultant doesn't charge an hourly rate, has no ego, and is being constantly updated and improved upon. At no additional cost. In Part 1, The Portable Chemist's Consultant places particular emphasis on heterocyclic chemistry since this is the bedrock of society-shaping materials such as medicines and agrochemicals. Beautiful interactive graphics are designed to rapidly solve your problems by being both immersive and rapidly absorbed. In Part 2, a broad coverage of solutions to the most encountered problems and issues of industrial chemists is presented

chemcompanion



Comments

FastROCS updated

I just got an email from OpenEye announcing an update to FastROCS.

FastROCS is an extremely fast shape comparison application, based on the idea that molecules have similar shape if their volumes overlay well and any volume mismatch is a measure of dissimilarity. It uses a smooth Gaussian function to represent the molecular volume [1], so it is possible to routinely minimize to the best global match.

Features

  • Processes 2 million conformations per second on a Quad Fermi box
  • Returns overlays based on the quality of the 3D shape match against the query
  • Overlays are intuitive and visually informative when viewed in standard visualizers (e.g. VIDA)
  • Available as an XML-RPC based web service
  • Jobs can be launched and the subsequent results viewed directly from within VIDA
  • Reports rigorous Tanimoto measure between shapes

fastrocs



Comments

A Pan Assay Interference Compounds (PAINS) Filter for filter-it

A Pan Assay Interference Compounds (PAINS) Filter for filter-it

Jonathan B. Baell and Georgina A. Holloway published a very interesting paper on their analysis of frequent hitters from screening assays. DOI

This report describes a number of substructural features which can help to identify compounds that appear as frequent hitters (promiscuous compounds) in many biochemical high throughput screens. The compounds identified by such substructural features are not recognised by filters commonly used to identify reactive compounds. Even though these substructural features were identified using only one assay detection technology, such compounds have been reported to be active from many different assays. In fact, these compounds are increasingly prevalent in the literature as potential starting points for further exploration, whereas they may not be

In the supplementary information they provided the corresponding filters in Sybyl Line Notation (SLN) format, unfortunately I don’t use SYBYL and so needed them in SMARTS format for use with filter-it.

This article describes the process of creating a .sieve file for use with filter-it.



Comments

AmberTools13 (released on April 22, 2013)

AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations (using NAB or mdgx), with either explicit water or generalized Born solvent models. It includes

NAB to build molecules; run MD or distance geometry, using generalized Born, Poisson-Boltzmann or 3D-RISM implicit solvent models. Antechamber and MCPB Create force fields for general organic molecules and metal centers, tleap a basic preparation program for Amber simulations. sqm semiempirical and DFTB quantum chemistry program. pbsa Performs numerical solutions to Poisson-Boltzmann models. 3D-RISM Solves integral equation models for solvation. mdgx Code for explicit solvent molecular dynamics simulations. ptraj and cpptraj Structure and dynamics analysis of trajectories. MMPBSA.py and amberlite Energy-based analyses of MD trajectories.

AmberTools is distributed in source code format, and must be compiled in order to be used. You will need C, C++ and Fortran90 compilers. The distribution contains a Reference Manual in pdf format.

New features include

  • Greatly expanded and improved cpptraj program for analyzing trajectories;
  • New options for PBSA calculations, including new solvers and dielectric models;
  • Updates to MMPBSA.py, including access through NAB of two new GB models;
  • New documentation and tools for inspecting and modifying Amber parameter files;



Comments

Installing the Transatlantic-Proteomics-Pipeline package (TPP 4.6.2) under Mac OSX

I regularly seem to get questions about how to install various bioinformatics packages under Mac OS X and whilst I try to help this is not really my area of expertise so when I see detailed instructions on another site I tend to make a note.

The Trans-Proteomic Pipeline (TPP), is a suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to an open mzXML format. Unfortunately Mac OS X does not appear to be a supported platform, fortunately Bosco Ho has written very detailed instructions on how to install under Mac OS X here



Comments

Wizard Updated

Wizard the point-and-click statistical analysis for Mac has been updated.

The focus of this release is supporting several new import formats, including the oft-requested XLSX and Numbers document formats.

A major change in the product line is that reading and writing R files and generating R code has now "graduated" from the Pro version and is now available in the Standard version. But Pro users shouldn't feel left out: with this release, Support for importing binary SAS files and generating SAS code -- both features only available in the Pro version.

New Features:

  • Import XLSX spreadsheets
  • Import Numbers documents

New Features (Pro Version):

  • Import SAS binary files (.sas7bdat)
  • Import plain-text data with SAS commands (.sas)
  • Generate SAS model estimation commands

New Features (Standard Version):

  • Import/export R files
  • Generate R commands

Bug fixes

  • Fix a crash when zero observations are included in the Model view
  • Fix a bug when importing multiple sheets in XLS documents
  • Fix a bug where Q-Q plots were not properly exported as PDF

There is a listing of data analysis tools for the Mac here.



Comments

BBEdit and regular expressions

I use BBEdit extensively but only need to use regular expressions infrequently, whenever I do I seem to spend a while getting the syntax correct. I’ve just come across the cheatsheet which I suspect I’m going to find invaluable.



Comments

ADF2013 released

I just got an email from CCL highlighting the release of ADF2013.

SCM is proud to announce the 2013 release of the ADF modeling suite. We continue to improve and expand our software suite with the aid of our academic and industrial ADF authors and other partners. Several enhancements and new features have been implemented in our molecular Density Functional Theory (DFT) code ADF and its periodic DFT companion BAND. Our semi-empirical Density Functional based Tight-Binding (DFTB) module has been updated and we offer Dr. Stewart's latest MOPAC2012 module including the PM7 model. The parallelization of the reactive MD module ReaxFF from van Duin and co-workers has been improved considerably.

There is more information here

ADF

I also noted there is a free 30-day trial available

Fully functional versions of all modules of our 2013 release are available free of charge for a 30-day evaluation period. The programs may be run on any machine at your organization, with full support. Just fill out our Free Trial Form. Other questions? : e-mail us at info@scm.com.



Comments

ChemDraw and Word compound numbering on Mac

A while back I got this question

”I’m about to hit the tedious part of writing my chemistry PhD thesis in Microsoft Word: having all mentioned compounds numbered in text and in the chemdraw imported files. My question: is there any automated option for this task or do I have to insert every number manually? In particular renumbering after adding a new compound in the middle of the text”

There are a couple of ways to do this in LaTex (http://www.jkwchui.com/2010/03/writing-chemistry-with-latex-33/) and (http://piti.exroot.org/konwerter/) but in my experience LaTex is not particularly popular among chemists. However help is at hand, I’ve just been sent details of a brilliant applescript that works with ChemBioDraw and Word.

The process is described in detail here (http://www.martinp23.com/blog/2013/03/chemdraw-and-word-compound-numbering-on-mac/) so I won’t give anymore details just to add that one thing I’ve been using in recent Chemdraw scripts is

tell application id "com.cambridgesoft.ChemDraw"

It avoids the problems with application naming with different versions of Chem(Bio)Draw Std/Pro/Ultra.

There are many more applescripts here.



Comments

Papers2 version 2.5 released

There has been an update to the very popular reference management application Papers2, this update introduces two new annotation styles (underlining and strikethrough). The meat of this update is focused around bug fixes and performance enhancements however, for example they have reworked spotlight indexing to be more robust, improved iOS syncing performance, and fixed a number of crashes. It also contains a number of smaller but significant improvements.

Performance improvements

  • Significantly improved performance of switching between collections.
  • Scrolling large number of collections is now smooth again.
  • Improved performance and reliability of iOS PDF syncing.
  • Improved performance of autocitekey generation.

In the release notes:-

We advise to upgrade to Papers for iOS 1.9.17, this free update is available in the iTunes App Store.

There is a list of reference management tools here.



Comments

Software from Open Chemistry

The Open Chemistry Group have just announced the availability of the first beta release of a suite of software packages for chemists.

It consists of Avogadro 2 an update to the well established molecular editing package, see a recent paper describing it for more details “Avogadro: an advanced semantic chemical editor, visualization, and analysis platform” DOI.

Some notable new features of Avogadro 2 include:

  • Scalable data structures capable of addressing the needs of large molecular systems.
  • A flexible file I/O API supporting seamless addition of formats at runtime.
  • A Python-based input generator API, creating an input for a range of quantum codes.
  • A specialized scene graph for supporting scalable molecular rendering.
  • OpenGL 2.1/GLSL based rendering, employing point sprites, VBOs, etc.
  • Unit tests for core classes, with ongoing work to improve coverage.
  • Binary installers generated nightly.
  • Use of MoleQueue to run computational codes such as NWChem, MOPAC, GAMESS, etc.

The second component of the suite is MoleQueue, a new tool to manage and execute computational tools either locally or on a remote machine or cluster. The messages transmitted between the client and server are formatted use the increasingly popular JavaScript Object Notation (JSON) format and adhere to the JSON-RPC 2.0 specification.

The final element of this first beta release is a chemically aware database MongoChem built on MongoDB intended to address the need for researchers and groups to be able to effectively store, index, search and retrieve relevant chemical data. It uses Open Babel to provide the cheminformatics input

There is a slide presentation describing the project in more detail here/



Comments

ElementalDB Updated

I just noticed an ElementalDB update appear on my iPad.

According to the release notes there have been substructure search performance improvements.

ElementalDB allows you search and explore the 1.2 million structure CHEMBL database locally on your iPad.

There is a review here.

photo



Comments

A couple of Updates

Marvin 5.12.3 has been released with a couple of bug fixes

Import/Export

  • Name to Structure (n2s)
  • Names with ylium and uide suffixes are now supported.

Calculation NMR (HNMR, CNMR Prediction, ...)

  • Coupling of a nucleus with a group of magnetically equivalent nuclei was not handled properly.
  • NMR Predictor did not consider negative coupling constant values.

JSDraw has been updated as part of the Cheminformatics DevSuite 2.5.1 Release.

There is an online demo of 3D structure generation here using JSME and JSmol.



Comments

Open Babel talk

Noel O’Boyle gave a brief talk at the New Orleans ACS describing the new features and plans for Open Babel

http://baoilleach.blogspot.co.uk/2013/04/talk-on-open-babel-at-new-orleans-acs.html



Comments

ChemDoodle Mobile Updated

I just noticed that an update for ChemDoodle was available on my iPhone.

According to the release notes this includes

  • Support for the iPhone 5
  • IUPAC Naming
  • 3D coordinate generation and viewer
  • Added empirical formula to calculations
  • Added rotatable bond count to calculations
  • Added total electron count to calculations
  • Added vdW volume to calculations
  • Added complexity to calculations
  • Fixed slow performance issues on iPad in landscape mode
  • Fixed MolGrabber search issues
  • Fixed issue where the back button wouldn’t appear on the last help page
  • Fixed login issues
  • Performance improvements
  • General improvements and fixes

There is a page of mobile science applications here.



Comments

A Review of StarDrop 5.3

I’ve just written a review of Stardrop an application from Optibrium that was designed to aid decision making for scientists involved in drug discovery that has recently been updated.

  • Virtual Library Enumeration – The Nova plug-in module for StarDrop now has the added ability to quickly and easily enumerate a virtual library based on a template scaffold that you define with substitution points and variable fragments. You can sketch the groups to substitute at each point, select them from a user-defined or centrally administered library, or take them from a decomposition of another series using the R-group analysis tool in StarDrop
  • Data visualisation - now allows you to apply interactive filters to your graphs and plots to quickly focus on the most interesting compounds. StarDrop now also supports the analysis of dates allowing you to explore variations of properties or scores with time
  • Clustering - this new tool enables you to easily identify groups of similar compounds within a data set, based on either their structural similarity or properties
  • Dataset Filtering - this helps you to remove compounds from a data set with unwanted sub-structures or property values. You can define any number of criteria with which to filter a data set
  • Duplicate Removal - when combining compound data from multiple sources it’s common to end up with multiple copies of the same compound in a single data set. The duplicate removal tool makes it easy to find these and choose the entries that you want to keep.
  • ADME QSAR – new model for predicting log([Brain]:[Blood]) (the old model remains available for consistency with previously calculated results)
  • StarDrop now includes a FieldAlign module, using Cresset's molecular Field technology, provides a unique, 3-dimensional (3D) insight into the biological activity, properties and interactions of your compounds.

There is a comprehensive list of software reviews here.



Comments

BBEdit Updated

My preferred text editor has been updated, this release consists entirely of fixes for reported issues, and contains no new features, nor changes to existing features,

As ever the release notes contain a few things to make you smile.

The display glyph for invisible spaces (when "Show Invisible" and "Show Spaces" are both turned on) is now U+00B7 (MIDDLE DOT). If spaces don't display when those settings are turned on, then your display font is missing that glyph, and you should report it to your font's developer as a bug. (I would have used U+1427 (CANADIAN SYLLABICS FINAL MIDDLE DOT) for the humour value alone, but not enough fonts supported that glyph. Sorry.) …

Fixed case in which PHP line comments inside of single-line directives (e.g. ?php ... // hello world foo bar ?, you can't make this stuff up...) would cause the PI closer to be missed and subsequently mess up color scanning.



Comments

ACCEPT-NMR

Accept-NMR uses an input PDB file, generate symmetry-related copies of a biological molecule of interest, and predict specific user-defined classes of intermolecular contacts between these (using a user-defined distance cutoff). Sort and analyze the resulting contacts, and visualize the results using several visualization schemes in PyMOL. Predict NMR spectra, and specifically the positions of intermolecular contact cross-peaks, based on the contacts predicted and chemical shift table. It is written in Perl, utilizing Gtk2-Perl bindings to provide a cross-platform compatible graphical user interface,

Added to the Spectroscopy page.



Comments

MayaChem tools updated

MayaChemTools: An open source package for computational discovery, COMP poster #306, 243rd ACS National Meeting & Exposition, March 25-29 2012, San Diego, CA

The current release of MayaChemTools provides command line PERL scripts for the following tasks:

  • Manipulation of SD, CSV/TSV, Sequence/Alignments and PDB files
  • Analysis of data in SD, CSV/TSV and Sequence/Alignments files
  • Information about data in SD, CSV/TSV, Sequence/Alignments, PDB and fingerprints files
  • Exporting data from MySQL, Oracle and PostgreSQL tables into text files
  • Properties of periodic table elements, amino acids and nucleic acids
  • Elemental analysis
  • Support for multiple valence and aromaticity models
  • Generation of fingerprints corresponding to atom neighborhoods, atom types, E-state indicies, extended connectivity, MACCS keys, path lengths, topological atom pairs, topological atom triplets, topological atom torsions, topological pharmacophore atom pairs and topological pharmacophore atom triplets
  • Generation of fingerprints with atom types corresponding to atomic invariants, DREIDING, E-state, functional class, MMFF94, SLogP, SYBYL, TPSA and UFF
  • Calculation of similarity matrices using a variety of similarity and distance coefficients
  • Calculation of physicochemical properties including rotatable bonds, van der Waals molecular volume, hydrogen bond donors and acceptors, logP (SLogP), molar refractivity (SMR), topological polar surface area (TPSA), molecular complexity and so on
  • Similarity searching using fingerprints

I’ve written a script for Vortex that uses MayaChem tools to calculate molecular properties.



Comments

ElementalDB on AppStore

ElementalDB is now available on the AppStore.

https://itunes.apple.com/app/elementaldb/id627422287

Sketch and search within the 1.2M compound ChEMBL 15 dataset. Searching, property calculation and depiction is done from the stored 2D co-ordinates from ChEMBL within the app on your device



Comments

A comparison of clipboard managers

This is an update to a blog post from early 2012.

For many years I’ve used the excellent Clipboardsharing to exchange the clipboard contents between my laptop and desktop machines, it also supports multiple clipboards. However it is not supported under Mac OS X 10.7.x (Lion) and the developer website seems to have disappeared. I spent a while looking at various alternatives and I thought I’d summarise my findings.

I should add I had a pretty clear view on my needs.

  • Exchange clipboard contents (text and images) between laptop and desktop machines running Lion
  • Have multiple clipboards
  • Ability modify text e.g. remove formatting

Nice to have

  • Keyboard shortcuts
  • Option to encrypt clipboard contents before transfer
  • Also exchange clipboard contents with iOS devices

Clipboard Evolved

Clipboard Evolved features a clipboard-like window for managing clips, a menu bar icon, and now a cover-flow interface for quickly pasting clips. It supports both text and images, and Clipboard Evolved has eight "complex" animation options to choose from: Ripple, Copy Machine, Star Burst, Irregular Holes, Disintegrate, Swipe, Crystallize, and Dissolve. It does not support clipboard sharing.

ClipMenu

ClipMenu is a clipboard manager that supports a number of text and images types including Plain text, Rich Text Format (RTF), Rich Text Format Directory (RTFD), PDF, Filenames, URL, TIFF image, PICT image. The clipboard history can then be accessed via an icon in the menu bar or via a shortcut key. ClipMenu can manage re-usable text as snippet. You can select it from menu and paste it anytime. It does not support clipboard sharing.

Clips

Clips automatically generates and arranges copied items into Application-specific clipboards, these can then be accessed via a Finder like interface or via an icon in the menu bar. It also supports live search so you don’t have to scroll through them, just start typing in the Clips Board or Organizer and non-matching items will fly off the screen instantly. It does not support clipboard sharing.

Clyppan

Clyppan is a clipboard history application that keeps a list of text you have copied to the clipboard, these can then be accessed via an icon in the menu bar. Clyppan only supports text clippings, but the history is searchable and pressing the spacebar will give you a Quick Look-style preview of the clipping, it also does not support clipboard sharing.

CopyLess

CopyLess supports all data types supported by the Mac OS X clipboard and has inline searching and Quicklook integration to allow you to check what you are pasting, it also keeps track of the application the data was copied from. It does not support clipboard sharing.

CopyPaste Pro

CopyPaste Pro is a popular clipboard history tool that can then be accessed via an icon in the menu bar or a graphical browser, CopyPaste Pro also has a selection of clipboard tools that allow the user to manipulate the data on the clipboard. It also allows the creation of archives to store clips for later use. It does not support clipboard sharing.

CuteClips3

CuteClips 3 is a recent update, it supports text and images which can then be selected from a list. It supports shortcuts and has an extensive list of keyboard shortcuts for manipulating the list and pasting options. It does not support clipboard sharing.

iClip

iClip supports copying plain-text, rich-text, images, audio, video, or files and all can be accessed in a rather neat iClip dock that sits on the side of the screen, you either drag and drop to and from the iClip history bins or copy and paste. It is possible to preview images in clip bins which might be very useful if you are working a lot of the time with images. It supports keyboard shortcuts, but does not have clipboard sharing.

Jumpcut

Jumpcut is an open source application that provides multiple clipboards. Every time you copy some text it is added to the Jumpcut stack, these can then be accessed via a scissors icon in the menu bar. Alternatively you can view the list via a hot-key. It does not however support images and as far as I can tell no plans for clipboard sharing.

Paste Master

Paste Master is configured by a preference pane that allows you to save multiple clipboards and be able to paste them again later, it displays the clipboards in a grid display, there is also access via a menu bar icon. Paste Master recognises certain text types, URLs, phone numbers, addresses and allows formatting as you paste. There is the option to save particular sets of clipboards, and several hotkey options. There is no clipboard sharing.

PTHPasteboard Pro 4

PTHPasteboard is comprehensive clipboard manager that supports multiple text and image clipboards, these can then be accessed via a customisable icon in the menu bar or from a floating window, clicking on an item in the clipboard history displays the application that the data was copied from and for text items shows the number of lines/words/characters and for images the size. PTHPasteboard also supports filtering of clipboard text allowing you to convert to unformatted text, convert to lower/upper case, change to Mac/Unix/Windows line endings. There is also a custom filter dialog that allows you to build your own filters for example to convert a list from a text document into an html list. It also allows the creation of custom clipboards. PTHPasteboard PRO's Syncing support takes advantage of Mac OS X's Bonjour technology to seamlessly sync your pasteboard items across multiple machines.

Savvy Clipboard

Savvy Clipboard holds a list of items that you copied — text fragments, graphics, URLs, multimedia data, or links to files — and lets you access them using this list from either a floating window or menu bar icon. You just select the needed item from the list, and it is ready to use from the system Clipboard, so you can paste it anywhere you want. While it is possible to export a list and transfer to another computer it does not support clipboard sharing.

ShadowClipboard

ShadowClipboard is another fairly comprehensive application, with unlimited clipboard sets, clipboard sharing, clipboard filtering and clipboard set backups, the clipboard history can then be accessed via an icon in the menu bar or from a window. It supports keyboard shortcuts, and shadowClipboard uses Apple's ZeroConf networking called Rendezvous. shadowClipboard clients will automatically recognise each other on a local network.

Stuf 2

Stuf 2 has a different way to share clipboards in that Stuf stores your clippings and can share them with any other Stuf users, even in a different country, with your permission of course. Stuf can use any network drive to share clippings, but they really recommend you use DropBox. Stuf 2 is available for both Mac and PC. It supports text and images and clipboard history can then be accessed via an icon in the menu bar.

So I bought PTHPasteboard which best meets my needs but obviously your needs may vary. There are also a couple of clipboard sharing tools Syncopy, which is nice because it supports Mac OS X and iOS, CrossClip which works between Mac, Linux and PC.

Comments

Chartsmith added to list of data analysis tools

I’ve just added Chartsmith to the list of data analysis tools.

Chartsmith is the premier charting and graphing application for Mac OS X. Built from the ground up on Mac OS X technologies, this application will make you and your data hum. Whether for scientific data visualization, for business presentation, or for graphics publishing, Chartsmith makes charting and graphing quick and easy.

scitech2

Chartsmith supports a variety of chart types and can import from Excel or ascii text files. There is also Applescript support for automating workflows.

There is a comprehensive listing of data analysis tools for Mac OS X here.



Comments

Marvin Updated

Marvin 5.12.2 has been released with a couple of bug fixes

Molecule Representation

  • Conversion from explicit hydrogen to implicit one removed stereo centers not having explicit hydrogen ligand.

Import/Export SMILES/SMARTS

  • Non ring bond information were imported as query strings from SMARTS.
  • After SMARTS import, those atoms that had no explicit aromatic property but had aromatic bond got query aromaticity property.



Comments

MathMagic Pro 8.5 updates

MathMagic Pro is a Mathematical equation editor that works well with any word processors, presentation software like Keynote or PowerPoint, DTP layout software like Adobe InDesign or QuarkXPress. Version 8.5 adds new Symbol fonts, direct drawing option for vertical and horizontal Fences for fine control over the Fence shape and thickness, new Plug-ins for InDesign CS5 ~ CS6 for batch applying of StyleSets to multiple equations within InDesign documents. InfoLogic also introduces a new conversion solution for InDesign generated XML and HTML files. This converter converts equations linked or embedded in XML/HTML files to MathML. adds various Frame types, more Sigma shapes, enhanced Fences, faster typing of script values & LaTeX expressions, and more.



Comments

ElementalDB

Way back in the distant past when I first joined the Pharma industry I remember working with a dumb terminal running sub-structure queries on a remote mainframe that seemed to take for ever on our relatively modest corporate database, returning the results would then bring our network to a crawl much to the annoyance of my colleagues. I’ve just downloaded ElementalDB from Dotmatics, this an iPad application that does a substructure search of a 1,200,000 structure database in less than a second.

Read more here.



Comments

Marvin 5.12.1 released

New features and improvements

Import/Export

S orbitals and oval shaped s or p orbitals are imported from CDX/CDXML.

Bugfixes

Painting, Charge symbol on carbon atoms was missing when the atom numbers were visible and the display of carbon atom labels was turned off. When two atoms had more than one electron flow arrows between them, the electron flow arrows overlapped each other. The second electron flow arrow started from a wrong position when a single electron and an electron pair flow arrow started from an atom which had a lone pair and a radical as well.

Editing, Atom Lists and NOT Lists could not be created by typing atomic symbols separated with commas (e.g., "f,br,cl" or "!f,br,cl").

Import/Export, MRV and CML export wrote out characters incorrectly which are not supported by the character set. SDF files having invalid header could not been imported. Deuterium and tritium isotopes were converted to simple hydrogen atom if a molecule was exported to ChemAxon compressed MOL format (CSMOL). MolExporter.exportToObject() added an extra newline to SMILES. Nitrogens connecting two aromatic rings had radical after import if nitrogen was bracketed in the SMILES representation. Absolute stereo flag was missing during InChi export/import and InChiKey export.

Molecule Representation, Number of added implicit Hydrogen atoms were incorrect in some cases for positively charged sulfur atom.

Calculation, After canonical tautomer generation, the information of "double cis or trans" bond type might have been lost in certain cases.



Comments

AppleScriptObjC Explorer Updated to version 2.5

AppleScriptObjC Explorer is a script editor that takes advantage of AppleScript’s ability to call Cocoa methods in OS X 10.6 and later. AppleScriptObjC — AppleScript with the added ability to call MacOS X’s Objective-C-based frameworks using AppleScript syntax.

New in AppleScriptObjC Explorer 2.5.0

  • Script stepping. You can now step through scripts a statement at a time using new Step, Resume and Resume to Selection commands.
  • Updates to exported apps. Exported apps get individually named executables, plus correct name in their application menus.
  • Bug fixes. Fixes to compiling, saving as .applescript files, and logging time-stamps.

There more details on the Applescript Resources Page.



Comments

Electronic Lab Notebook

I occasionally get asked about electronic notebooks, many seem to be somewhat inflexible and don’t support the range of modern mobile devices that are now used routinely. I keep an eye out for web-based solutions since these look to be a better option in a varied platform environment.

I just noticed the Electronic Lab Notebook from Sciformation. It seems to be web-based using pre-installed templates, which are XML documents, these are quite simple to design more custom-made templates.

Dotmatics also have a web-based Electronic Lab Notebook that covers all scientific disciplines in a single interface including chemistry and biology experimental data.



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TB Mobile

There is an interesting article in the Journal of Cheminformatics regarding an app I’ve highlighted previously, TB Mobile: a mobile app for anti-tuberculosis molecules with known targets.

TB Mobile may assist researchers as part of their workflow in identifying potential targets for hits generated from phenotypic screening and in prioritizing them for further follow-up. The app is designed to lower the barriers to accessing this information, so that all researchers with an interest in combatting this deadly disease can use it freely to the benefit of their own efforts.

tbmobile

There are more mobile science applications listed here.



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Four new mobile science apps

Four new mobile science applications from ZappyLab a provider of mobile and web applications for scientists. They focus on creating tools that are helpful to researchers and laboratory workers.

GrowthCurves is a portable spreadsheet for researchers working with cell cultures.

PubChase is a science literature search and recommendation tool, available online or on your mobile device

Lab Counter is a tallying app, specifically designed for the scientists and medical laboratory workers.

Tetrad is a utility for yeast geneticists to score yeast tetrad dissections.

They have all been added to the mobile science page.



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GPU accelerated version of GROMACS 4.6

I thought I would give a plug to an upcoming webinar that Dr. Erik Lindhal at Stockholm University and NVIDIA are presenting to discuss latest GPU-acceleration technologies available to GROMACS users. Join to learn about latest accelerated version of GROMACS 4.6, which features are supported, it's installation and use, and how it performs with latest NVIDIA Kepler GPUs.   The webinar is planned for Thursday, April 4th, 2013 9:00 AM - 10:00 AM Pacific Standard Time

Register here: goo.gl/ioQMd

There is a list of GPU accelerated application here



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UnityMol games engine based molecular viewer

When you compare the amount of resources and effort that goes into computer games with the amount that is available for scientific software it is clear that the games industry wind hands down. It is not surprising therefore that some enterprising scientists are looking at leveraging games technologies to build new applications.

You can read more here Game On, Science - How Video Game Technology May Help Biologists Tackle Visualization Challenges

The video games industry develops ever more advanced technologies to improve rendering, image quality, ergonomics and user experience of their creations providing very simple to use tools to design new games. In the molecular sciences, only a small number of experts with specialized know-how are able to design interactive visualization applications, typically static computer programs that cannot easily be modified. Are there lessons to be learned from video games? Could their technology help us explore new molecular graphics ideas and render graphics developments accessible to non-specialists?

For an example application have a look at:-

UnityMol is a molecular editor, viewer and prototyping platform, coded in C# with the Unity3D game engine. It was developed by Marc Baaden's team at the LBT laboratory at the IBPC institute of CNRS in Paris. UnityMol includes HyperBalls designed to visualize molecular structures using GPU graphics card capabilities based on shaders (GLSL or Cg). UnityMol can currently read Protein Data Bank (PDB) files, Cytoscape networks, OpenDX potential maps and Wavefront OBJ meshes.



Comments

SAR Table updated

The SAR Table app has had the ability to match scaffolds to molecules for a while now, but as of the latest release (1.3.4) just submitted to the AppStore, it will be able to match more than one scaffold at once. The actual process of performing the scaffold match is provided by a webservice (molsync.com).

More details here.



Comments

OpenMM Updated

OpenMM has been Updated

OpenMM is a toolkit for molecular simulation. It can be used either as a stand-alone application for running simulations, or as a library you call from your own code. It provides a combination of extreme flexibility (through custom forces and integrators), openness, and high performance (especially on recent GPUs) that make it truly unique among simulation codes.



Comments

Publication Quality Chemical Structures

There are two main occasions when a chemical drawing package is needed, firstly as a front-end to a chemical database for creating structure-based queries, and secondly for creation of chemical structures in publications. Whilst many drawing packages are fine for query construction some are far from ideal for creating publication quality output.

This paper from Alex Clark (DOI: 10.1002/minf.201200171">10.1002/minf.201200171) discusses the issue in detail.

The creation of 2D molecular structure diagrams that make full use of the capabilities of modern display systems, using only input data expressed in file formats used for cheminformatics, is a complex task that requires a number of additional algorithms. Assuming that atom positions have been well chosen, the rendering engine is required to micromanage the precise positioning of atom labels, bonds and atom adjuncts, in such a way that the final output is correct, consistent with convention, and as pleasing to the eye as a diagram produced by a graphic designer. The techniques must be equally applicable when creating output for low-resolution screens and high resolution printed output, and make use of contemporary graphics file formats in such a way that the largest possible number of software platforms are able to display the output at any resolution without degradation or inconsistency. The main issues involved in meeting these criteria are discussed, and algorithms for satisfying them are presented.



Comments

Accessing the Chemical Identifier Resolver from Marvin

With the release of Marvin 5.12.0 users can now also access a custom web-service to extend name to structure conversion - for instance, with corporate IDs or common name dictionaries. I thought it might be useful to have a look at this new feature however I don’t have a corporate web service that I can use. This is where use of the Chemical Identifier Resolver (CIR) comes into play



Comments

Marvin 5.12.0 has been released

Marvin 5.12.0 has been released. This has an important updates for Mac OS X users, in that image to structure conversion using OSRA and text OCR for scanned documents is now supported on Mac OS X.

OCR_OSR

In addition Structure Checker configuration can be accessed via URL from MarvinSketch, Structure Checker application, and via Structure Checker API call. Users can now also access a custom web-service to extend name to structure conversion - for instance, with corporate IDs or common name dictionaries. Typing abbreviated group names is now case sensitive, When pasting unrecognised format onto the canvas, "Import as" dialog appears, and the user can choose the correct format. Structures can be copied as "Daylight SMARTS" and "ChemAxon SMARTS (CXSMARTS)" formats. The MMFF94 forcefield has been added to Generate3D and can also be used in the Conformer Plugin and Molecular Dynamics Plugin.

The complete release notes are available here



Comments

Evernote as an ELN

There is an interesting blog entry by Rich Apodaca on Depth-First talking about using Evernote as an Electronic Lab Notebook (ELN). I’ve been involved in several discussions about using an iPad as an ELN and one thing that always comes up is data entry.

The major issue from both those who use an ELN and those who have decided against using an ELN is they want to be able to freehand draw structures and notes directly into the notebook.

To partially overcome this you can use Notability on an iPad and this Dropbox workflow to incorporate hand drawn notes into a Evernote notebook. However to date whilst using your fingers or stylus makes a passable job of text input I’m less than impressed with the ability to draw chemical structures quickly and accurately. If anyone has suggestions for a stylus that allows the user to draw chemical structures accurately I and many others would be interested. The main issue is trying to select points on the end of bonds, ideally you need a sharp pointed stylus.



Comments

Wizard Pro updated

The data analysis tools Wizard and Wizard Pro have been updated to improve blank cell detection during excel imports.

Wizard supports the most common statistical tests and models, including...

Univariate Tests Shapiro-Wilk test of normality , 1-sample Kolmogorov-Smirnov (normality and uniformity) , Pearson's goodness-of-fit (equal proportions)

Bivariate Tests Pearson's goodness-of-fit (chi-square) , t-test and ANOVA , Correlation (Pearson product-moment) and R² , Mann-Whitney and Kruskal-Wallis , 2-sample and N-sample Kolmogorov-Smirnov

Multivariate Models Linear regression (OLS) , Weighted linear regression (WLS) , Poisson and geometric regression , Logistic regression (Logit) and Probit , Multinomial Logit and Ordered Probit , Negative Binomial (NegBin-2) , Cox Proportional Hazards

Regression Features Fixed effects , Robust standard errors , Clustered standard errors , Joint significance tests , Odds ratios , Residual analysis , Interactive prediction assistant

There are many more data analysis tools for Mac OS X here.



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Another markdown editor

I’ve previously highlighted a number of Markdown editors and I was recently sent a link to another. Marko is a rather different application, you use Marko side-by-side with your favourite text editor to preview your Markdown documents as you write and it automatically reloads when you save your changes. It also exports well-formatted HTML or PDF, Copy plain HTML source code and supports Github Markdown extensions.



Comments

Smina

Smina is a fork of AutoDock Vina that is customized to better support scoring function development and high-performance energy minimization. smina is maintained by David Koes at the University of Pittsburgh and is not directly affiliated with the AutoDock project.



Comments

DEVONthink 2.5

DEVONthink 2.5 now has syncing and web sharing

Sync-icon

Using multiple computers, working from different places, sharing data with coworkers: In today’s highly connected world it’s essential to always have access to the latest data. And because we know that, of course, we worked hard on creating the most versatile yet robust synchronization technology and rewriting the build-in web server of DEVONthink Pro Office. All editions of DEVONthink 2.5 synchronize databases between multiple computers and locations either directly or via Dropbox, WebDAV, file servers, or just any mountable disk. The new web server gives your PC and Linux colleagues access to the databases you want to share with them directly through their favorite web browser. And if you’re still fighting the paper flood you will like the enhancements we have made to the scan feature

There are more reference management applications here.



Comments

WaveMetrics Updates

XOP Toolkit 6.30 is now shipping. This release adds support for Xcode 4.3.2 through 4.6 and for Visual C++ 2012. This release is mostly to keep up with Xcode 4 changes and to add Visual C++ 2012 sample XOPs and documentation. As described in the release notes (Appendix C of the XOP Toolkit 6 manual), a side-effect of keeping up with Xcode 4 is that XOPs compiled by XOP Toolkit 6.30 require Igor Pro 6.20 or later. The requirement of Igor Pro 6.20 is the reason for bumping the XOP Toolkit version from 6.02 to 6.30. "6.30" was chosen because that is the contemporaneous Igor version. If you are a licensed XOP Toolkit 6 user, this is a free update.

IGOR Pro 6.3 has been updated.

New Features

Added a Batch Curve Fitting package: allows you to fit batches of data to the built-in or user-defined fitting function of your choice. A "batch" is a collection of similar data sets stored in waves to which a common fitting function, initial conditions, and weighting and masking waves have been applied. Each data set may be stored in a waveform, an XY pair, or in the columns of a 2D wave. Added the Scatter Dot Plot Panel. Scatter Dot Plots are one part category plot, one part scatter plot, and one part histogram. Like category plots they show total counts for multiple data sets, each labeled on the X axis. Like scatter plots they provide a sense of the data's distribution. Like histograms they sort data into bins of points in which all values fall into a range. The Multipeak Fitting 2 package now supports constraints on peak coefficients. NewImage supports direct RGBA color image plots. The FilterFIR notch filter length had been limited to 4001 points. Now the limit is 2147483647 points, which makes the minimum notch width 0.000107% of the sampling frequency.

There is a page of data analysis tools here.



Comments

Molecule Calculator

After I wrote the article about javascript based molecule viewers I’ve been sent a couple of links demonstrating their use. One particularly interesting one is MolCalc an online molecular calculator that uses JSmol to build and render structures.

molcalc1

Once the molecule has been built and minimised using the MMFF force field you can then use GAMESS to calculate a range of molecular properties.

molcalc2

MolCalc is distributed through GitHub under the GPL license github.com/jensengroup/molcalc. You must obtain a copy of the GAMESS code separately from www.msg.ameslab.gov/gamess/download.html Since this uses javascript for the interface it will work on mobile devices.



Comments

Mnova 8.1.1 released

Mnova 8.1.1 is a minor release that fixes several bugs in Mnova NMR, MS and the installation process.

New Features
Capability to update gamma value of a DOSY spectrum depending on the detected nucleus

Bugs Fixed

  • Withewashed view looked wrong in 2D spectra
  • Peaks integrated using Peaks method did not get deleted
  • Problem copy/pasting a spectrum from Mnova to MS Word as OLE
  • Wrong order on assignments reported by Assignments script
  • Problems opening a document with deleted molecules and with the compounds table linked to the Page Navigator

There is a page of spectroscopy applications for the Mac here.



Comments

StarVue Review

I’ve just written a brief review of StarVue.

StarVue is a free (requires registration) chemical structure viewer from Optibrium.

coverflow

More Reviews and Tutorials



Comments

Elemental for iPad/iPhone updated

Dotmatics have announced an update to their chemical sketching application Elemental to version 1.5. No details of any changes are available.

There is a page of mobile science applications here.

Chocolat a text editor for Mac OS X, that combines native Cocoa with powerful text editing tools has been updated.

There are more text editors here.



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Scripting Vortex 12

In the previous tutorial we made use of the Virtual Computational Chemistry Laboratory web service to calculate aLogP and LogS, both these results were returned in a simple text format. More recently there has been an increased use of JSON format for data exchange.

JSON, or JavaScript Object Notation, is a text-based open standard designed for easy human-readable data interchange. It is derived from the JavaScript scripting language for representing simple data structures and associative arrays, called objects. Despite its relationship to JavaScript, it is language-independent, with parsers available for many languages including including C, C++, C#, Java, JavaScript, Perl, Python.

Molinspiration provide a number of cheminformatics tools but also provide a RESTful web service these web services can be used to calculate a range of molecular properties and bioactivity predictions.

The output from both web services is available either as a JSON string or plain text, the web service can be accessed by submitting a URL

Full details of the script are here.

vortex1



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Parallel Quantum Solutions

I’ve added Parallel Quantum Solutions to the alphabetical listings.

We estimate that well over 80% of CPU cycles spent in ab initio computations are used in optimizing geometries at the SCF or DFT levels,and in computing molecular properties, such as vibrational frequencies and NMR chemical shifts. Such calculations are extremely well suited for parallel implementation. Shifting them to an inexpensive and fast parallel machine can free up expensive workstations for more demanding calculations.




Comments

iBabel3

I’ve been slowly updating iBabel.

As you might have imagined the issues with Java security have made it impossible to support the use of Java Applets as the molecule viewer so I’ve been busy trying out various options. I’ve decided to abandon the use of Java applets and the use of plugins; sorting out which version of a plugin works with which version of browser and/or operating system version was becoming a nightmare. So I’m moving to a variety of Javascript based molecule viewers.

There are now separate versions for Mac OS X 10.7.x and 10.8.x

More details on the iBabel3 page.



Comments

iNMR Reader for free

I noticed this in the iNMR newsletter.

FREE FOR EVERYBODY Only today 22nd Feb, anybody can ask for a free key for iNMR reader 5. No questions asked. iNMR reader 5 is a 64-bit application that requires Snow Leopard (or a later OS).

iNMR website

A new iNMR reader is available after many months. Instead of restarting from the old version, I have started from the full edition(which includes CPM, DOSY, relaxation times and many other things missing in the old reader), from which I have removed just three commands: Save, Export and Console. In practice it's the iNMR you have appreciated in the past year at a much lower price. Another thing that changes is the key: the old key isn't good. If you already have a license, please wait until March to install this new version and ask for the key. There is no upgrade fee to pay, but remember that a disposable license can't be moved to another computer. You will receive the key valid for your old computer. To ask for a new key, please send the old one back.





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Offsite backup options

Whilst I have an external hard drive for backups I used to use my dotMac account as my off site backup but with its closure I had to look for alternatives. I thought it might be useful to summarise my findings.

Backups are one of those things that seem pretty mundane until you really need the backup, and it always seems to occur at the most inconvenient time.



Comments

OpenEye Toolkits v2013.Feb

Just saw this announcement from OpenEye

OpenEye is pleased to announce that the OpenEye Toolkits v2013.Feb have been released. This release includes the C++, Python, .NET and Java versions of the Toolkits. Please see the release notes for specific details on the improvements and fixes made in this release.

  • OSX 10.8 support added for C++, Python, and Java. Note, C++ and Python are built with the Clang 4 compiler.
  • Visual Studio 2012 support added for C++ and C#.
  • OSX 10.6 32-bit python is no longer supported.
  • The next release, 2013.Jun, will be the last release to support SuSe 10.
  • The documentation examples were accidentally left out of the last release on Windows. They can now be found in C:\Python27\OpenEye-2013.Feb.1\docexamples.
  • Importing the python toolkits when there are spaces in the directory structure should now work properly.
  • Added the toolkit package version to the openeye module, e.g., openeye.version == "2013.Feb.x" for this release.



Comments

Cheminformatics on a Mac

I gave a talk at the Cambridge Cheminformatics meeting last week, I’ve put the slides here. It was more of a demonstration than a talk but the slides give an overview and links to the various tools.

Slide01

Updated

A couple of people have asked for a pdf version of the slides for download.



Comments

FTranProjectBuilder updates

I’m not a Fortran programmer so I’ve perhaps not as close an eye on this as other areas, however looking at the Fortran IDE FTranProjectBuilder release notes it seems there have been 17 updates in the last 12 months. FTranProjectBuilder is now up to version 1.15 with new features being added at a steady rate. Of note for scientists FTranProjectBuilder has support for two of the most common parallel processing libraries. If your program is coded for MPI using OpenMPI or OpenMP and you have them installed, you can use FTranProjectBuilder to run on multiple processors. 

editorview_med

These sites might also be useful

Fortran Compiler Instructions for OS X

High Performance Computing for Mac OS X

Installing C/C++/Fortran compilers on your Mac



Comments

Scripting Vortex:- Accessing a web service

I’ve just added the latest script for Vortex.

In previous scripts we have generated data using a local Java program, C program, PERL script, and SVL program. In this tutorial rather than have a local application generate the data we will use a web service.

mols

There are more scripts on the Hints and Tutorial pages.



Comments

BBEdit 10.5.2 released

My favourite text editor BBEdit 10.5.2 has a focused maintenance update which includes fixes for reported issues. This release consists entirely of fixes for reported issues, and contains no new features, nor changes to existing features.



Comments

Green Solvents updated

The latest version of Green Solvents (1.1) is now available on the AppStore. Worth noting is the fact that the app is now sponsored by the Royal Society of Chemistry.

There is a page of mobile science applications here.



Comments

Elemental for iPad/iPhone updated

Dotmatics have announced an update to their chemical sketching application Elemental. Version 1.4 includes an improved calculated properties engine.

photo

There is a page of mobile science applications here.



Comments

Open Molecular Mechanics (OpenMM) workshop

This might be of interest.

Simbios invites you to join us at its next Open Molecular Mechanics (OpenMM) workshop.

Where:  Stanford University When:   March 26-29, 2013 Registration:  Free but required and spaces are limited. To register or for more information, visit http://simbios.stanford.edu/MDWorkshop.htm.

OpenMM (http://simtk.org/home/openmm) is open-source software that enables molecular dynamics (MD) simulations to be accelerated on high performance computer architectures. It has demonstrated speed ups for both implicit solvent[1] and explicit solvent simulations[2] on graphics processing units (GPUs).  Its performance, openness, and extreme flexibility  via custom forces and integrators  make it truly unique among simulation codes.

A well-designed framework provides an application layer and a library, so that non-programmers can easily and quickly run MD simulations and develop custom algorithms on GPUs, while programmers are simultaneously able to integrate OpenMM cleanly into their own programs.

The workshop offers two tracks:  one for those who want to use OpenMM to run molecular dynamics simulations (no programming experience is needed), and another for programmers interested in integrating OpenMM into their own software.  

The last two days of the workshop are devoted to having the OpenMM team assist participants with their individual projects.   You can sign up for an instructional track, just the open working days, or both.  


OpenMM is supported by Simbios, an NIH National Center for Physics-Based Simulation of Biological Structures. To learn more about Simbios and its research and software tools, visit http://simbios.stanford.edu.

[1] OpenMM accelerated code running on NVIDIA GeForce GTX 280 GPU vs.  conventional code with Amber9 running on Intel Xenon 2.66 GHz CPU. MS Friedrichs, et al., "Accelerating Molecular Dynamic Simulation on Graphics Processing Units," J. Comp. Chem., 2009, 30(6):864-872.

[2]Eastman, P. and Pande, V.S., Efficient Nonbonded Interactions for Molecular Dynamics on a Graphics Processing Unit, J. Comp. Chem., 2010, 31(6):1268-1272.

There is a listing of GPU accelerated scientific applications here.



Comments

UCSF Chimera Version 1.7

UCSF Chimera Version 1.7 has been released. UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles.

New Tools:

  • APBS (Surface/Binding Analysis) — interface to Poisson-Boltzmann electrostatics calculations with APBS, using either a web service provided by the National Biomedical Computation Resource (NBCR) or a locally installed copy
  • AutoDock Vina (Surface/Binding Analysis) — interface to single-ligand docking with AutoDock Vina, using either a web service provided by the National Biomedical Computation Resource (NBCR) or a locally installed copy
  • Model/Refine Loops (Structure Editing) — interface to Modeller for building missing parts or refining existing parts (the former Model Loops tool only performed the latter and did not facilitate combining the refined and unchanged parts)
  • Notepad (Utilities) — allows entering descriptive text that can be saved along with sessions
  • PDB2PQR (Structure Editing) — interface to structure cleanup and charge/radius assignment with PDB2PQR, using either a web service provided by the National Biomedical Computation Resource (NBCR) or a locally installed copy



Comments

SZMAP v1.1.1 Released

OpenEye have announced that SZMAP 1.1.1 has been released. This is a bug fix release that repairs one major bug and several minor ones.

  • A rare but important bug in how the SZMAP application decides which apo grid points will be analyzed under certain circumstances has been fixed.
  • The metadata added to SZMAP output now includes the correct version number.
  • The position of points tested for stabilization by GAMEPLAN no longer differ slightly between different architectures.
  • Running GAMEPLAN from a directory containing the word "gameplan" works properly now.
  • The GRID_COMP utility now generates the appropriate subset of probe orientations for displacement operations.
  • The Water Orientation VIDA Extension now clearly identifies ligand or protein displacement entries in the selection pop-up menu.
  • The WaterColor VIDA Extension no longer switches the hypothesis molecule to wireframe when run while a hypothesis is selected in the list window.

SZMAP uses semi-continuum Poisson-Boltzmann electrostatics to map variations in solvent properties in a protein binding site. It identifies key waters, shows their interactions, compares them to the corresponding ligand atoms, and determines whether neighboring waters aid or hinder binding, giving insights into the role of water molecules in ligand binding. The included tool GAMEPLAN, suggests ways to modify ligand chemistry based on this understanding of water structure in the immediate environment of the ligand.

szmap



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Collaborative Computing Project for NMR updated

The Collaborative Computing Project for NMR was updated last night. No details are available.

The Collaborative Computing Project for NMR (CCPN) is a project that aims to bring together computational aspects of the scientific community involved in NMR spectroscopy of biological molecules, especially those who work in the field of protein NMR. The CcpNmr software suite is a series of programs for macromolecular NMR spectroscopy integrated with the CCP data model. Between programs written by the CCPN, external contributions, and ‘outside’ programs integrated with the data model, it is the intention to provide one suite of programs to carry out all tasks needed in macromolecular NMR spectroscopy. The nature of the data model guarantees that any other program or suite that interfaces with the data model can be used alongside or instead of the CcpNmr suite.

CCPN will be giving a demonstration at the EUROMAR conference during the first week of July (see http://www.euromar.org/). They will also be handing out CDs with the latest release.

There is a page of spectroscopy applications for Mac OS X here.



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Try MD/QC applications remotely on latest Tesla K20 GPU Accelerators for free

I just got this email from NVIDIA

Read the benchmark reports on how the Tesla K20 GPUs can increase application performance over the previous generation Fermi GPUs, and CPUs alone.
AMBER 12 Benchmark Report - http://bit.ly/AMBERGPU
NAMD 2.9 Benchmark Report - http://bit.ly/NAMD
GPU
LAMMPS Benchmark Report - http://bit.ly/LAMMPSGPU
GROMACS 4.6 Benchmark Reprot - http://bit.ly/GROMACS
GPU
To sign up for the free and easy Tesla K20 GPU test drive today and try AMBER on Tesla K20, all you need to do is: 1. Register on www.nvidia.com/GPUTestDrive 2. Log in to a remote cluster with Tesla K20 GPUs (we will send you instructions). 3. Run your application to get speed-up results for Tesla K20. Several MD/QC applications are already pre-loaded on the cluster. You can also try your code.

There is a listing of GPU accelerated scientific applications here.



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A busy time for mobile science

There are a couple of things happening in the mobile science space that I thought I should highlight.

The SAR Table app is going through some major improvements at the moment. The recently added matrix view is being modified to make it more interactive.

sartable

Recently the Mobile Molecular DataSheet (MMDS) was updated with the ability to parse ChemDraw files in particular it understands reaction schemes.

It can extract reaction schemes, and reassemble them into the more highly structured form that MMDS uses, i.e. segregated into individual components, where each distinct part of the reaction is characterised as a reactant, reagent or product, and is described by name/structure/both, and stoichiometry.

The ChemSpider synthetic pages reactions are stored in Chemdraw format and can thus be imported into MMDS, the sequence of actions is shown here

There is also a presentation by Antony Williams describing work at the Royal Society of Chemistry to support mobile science.



Comments

For those who complain about the Apple App approval process

News from thenextweb, a very sophisticated app on Google Play.

We’ve seen malware for PCs that infects mobile devices, but it turns out there’s also malware for mobile devices designed to infect PCs. Kaspersky researchers have discovered a new piece of Android malware that masquerades as a “cleaner” app meant to free memory for Google’s operating system but wreaks havoc on your smartphone in the background and on Microsoft’s operating system when it’s connected to a PC

There is related article that compares mobile threats here it looks like Android is being targeted.



Comments

OEDocking updated

OpenEye has announced the release of OEDocking v3.0.1. This is a bug fix release to the FRED, HYBRID, and POSIT programs. Of note, the report generated by both FRED and HYBRID has been significantly improved with this release

CHANGES

  • The program dockreport has been renamed to DOCKINGREPORT

NEW FEATURES AND IMPROVEMENTS

  • The formatting of the DOCKING_REPORT has been significantly improved and now includes:
  • Added a protein interaction fingerprint
  • XLogP
  • Polar Surface Area (PSA)
  • Improved the geometry detection for hydrogen bond protein constraints in FRED and HYBRID. These constraints should now be tighter.

BUG FIXES

  • Stereo isomer detection in POSIT was not handling bridgeheads properly, this caused some non-stereo molecules to be identified as such.
  • Fixed a bug in FRED and HYBRID where clash detection between hydrogen bonding groups was occasionally too strict.



Comments

The continued rise in mobile computing

The latest data from Net Applications is available and the continued rise in mobil computing is clearly seen. In January 2013 mobile devices account for nearly 12% of web usage, with iOS holding just over 60% and Android 24%. Blackberry languishes at under 2% and it remains to be seen whether there new offerings will revive the once market leading company. The iPad is the most popular mobile device followed by iPhone.

On the desktop it is pretty much unchanged, Windows still account for around 90% (with XP unchanged at 39%) and Mac just over 7%. Mac OS X 10.8 is the most popular Mac operating system.

There is a page of mobile science applications here.



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Displaying structures using JSmol and GLMol

I’ve previously highlighted the use of ChemDoodle web components to display molecular structures within a web page, and a recent publication DOI by Henry Rzepa lead me to explore some of the newer additions to the means to render molecules within a web page without the use of applets or plugins.



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Automating Exporting to Evernote

I had an interesting email from Geoff Hutchison who is using an iPad mini for taking notes using Notability the notes can be typed, handwritten using a stylus, or images. Notability does not export directly to Evernote an app that can capture and synchronise notes between multiple platforms including iPad and desktop. The other feature that makes Evernote interesting is it provides handwriting recognition, thus making the handwritten notes text searchable.

Geoff had a Automator service that imported the Notability notes that had been saved to Dropbox into EverNote, however he wanted a better way to name the notes created in Evernote. As it turned out the best way to do this was to use Applescript, you can read the full details here.



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StarDrop 5.3 is now available

Optibrium have just announced that StarDrop 5.3 is now available, including many new features, the highlights include:

  • Virtual Library Enumeration – The Nova plug-in module for StarDrop now has the added ability to quickly and easily enumerate a virtual library based on a template scaffold that you define with substitution points and variable fragments. You can sketch the groups to substitute at each point, select them from a user-defined or centrally administered library, or take them from a decomposition of another series using the R-group analysis tool in StarDrop
  • Data visualisation - now allows you to apply interactive filters to your graphs and plots to quickly focus on the most interesting compounds. StarDrop now also supports the analysis of dates allowing you to explore variations of properties or scores with time
  • Clustering - this new tool enables you to easily identify groups of similar compounds within a data set, based on either their structural similarity or properties
  • Dataset Filtering - this helps you to remove compounds from a data set with unwanted sub-structures or property values. You can define any number of criteria with which to filter a data set
  • Duplicate Removal - when combining compound data from multiple sources it’s common to end up with multiple copies of the same compound in a single data set. The duplicate removal tool makes it easy to find these and choose the entries that you want to keep.
  • ADME QSAR – new model for predicting log([Brain]:[Blood]) (the old model remains available for consistency with previously calculated results)



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Markdown Live

I use markdown extensively on my websites, “Markdown” is two things: (1) a plain text formatting syntax; and (2) a software tool, written in Perl, that converts the plain text formatting to HTML allowing you to build HTML documents in an easily readable form. I mainly use BBEdit and regard it as the “gold standard” but I keep an eye out for other markdown editors.

I added a recent addition Markdown Live to the list of available editors.



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OpenCL conference

I just noticed the announcement of the first International Workshop on OpenCL

The International Workshop on OpenCL (IWOCL) is an annual meeting of vendors, researchers and developers to promote the evolution and advancement of the OpenCL standard. The meeting is open to anyone who is interested in contributing to, and participating in the OpenCL community. IWOCL is the premier forum for the presentation and discussion of new designs, trends, algorithms, programming models, software, tools and ideas for OpenCL. Additionally, IWOCL provides a formal channel for community feedback to OpenCL promoters and contributors.

The closing date for submitting papers is Feb 8th

We solicit the submission of unpublished technical papers detailing innovative, original research related to OpenCL. All topics related to OpenCL are of interest, including OpenCL applications from any domain (e.g., scientific computing, video games, computer graphics, multimedia, information retrieval, optimization, text processing, data mining, finance, signal and image processing and numerical solvers), OpenCL performance analysis and modeling, OpenCL performance and correctness tools and proposed OpenCL extensions.

There is a listing of GPU accelerated scientific applications here.



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RapidMiner 5.3 released

RapidMiner v5.3 has been released. RapidMiner provides data integration, ETL, data analysis, and reporting in a single application, with an intuitive, drag and drop visual environment for designing and deploying customized analytical processes, and has been downloaded by over three million users worldwide.   In addition to over 100 performance, usability and stability improvements, the new version delivers more powerful data analysis operators and access to popular data sources including Microsoft Excel™ 2007 and SAS™. RapidMiner v5.3 is also fully integrated with the Rapid-I Marketplace, where users can discover and install new RapidMiner extensions published by a growing list of independent developers. Popular extensions include text and web mining, image mining and recommenders. Various Extensions for RapidMiner are available from the update server (go to the "Help" menu and select "Update RapidMiner")

RapidMiner v5.3 also features

  • More than 20 new functions for analysis and data handling, including multiple new aggregation functions;
  • File operators, including Move File, Rename File, Copy File, Create Directory, and Delete Files, directly from RapidMiner; and
  • A macro viewer that shows macros and their values in real time during process execution, for better debugging.

There is a comprehensive list of data analysis tools for Mac OS X here.



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SPRESImobile updated

With SPRESImobile, a wealth of chemical reaction information is readily available at your fingertips from a mobile device (iPhone, iPad). You can search the entire ChemReact database easily with this highly intuitive app

There is a page of mobile science applications here.



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Mobile Molecular DataSheet Updated

I just noticed that version 1.4.1 of the Mobile Molecular DataSheet (MMDS) has just been submitted to the iTunes AppStore, and its notable new feature is the ability to select a datasheet and calculate structure-based properties. A new column is created for each selected property, and the calculation feature is applied to each row. The available properties currently include molecular weight/formula, log P, molar refractivity and topological polar surface area. The functionality is provided by the molsync.com webservice.

There is more information on the Cheminformatics blog.

There is a page of mobile science applications here.



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SMARTCyp 2.4 released

The new SMARTCyp version 2.4 includes solvent accessible surface area (SASA) in the scoring function. SASA is computed using the 2DSASA algorithm from 2D coordinates.

smartcyp

  A paper describing the new models and their predictive accuracy on nine CYP isoforms is available in Molecular Pharmaceutics DOI



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Review of iScienceSearch

I’ve just published a review of iScienceSearch (iSS) an Internet search engine for chemists, it supports both chemical structure and text-based searches.

In addition to searching a wide range of databases it provides access to Chemicalize.org which gives access to chemical properties, and PASS (Prediction of Activity Spectra for Substances) to evaluate chemical structures.

There is a growing collection of software reviews here.



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Search integration added to MolPrime+

Database searching has now been added to MolPrime+ for iOS. The latest version, 1.1, has been submitted to the AppStore and should be available soon. As soon as it is approved, it will be possible to easily search the PubChem and ChEBI databases, by name or structure, and use the results within the app.

molpp_search1

There is a detailed description here

There many more iPhone/iPad apps on the mobile science page.



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Fen Zi GPU-based MD simulations

Fen Zi (yun dong de Fen Zi = Moving MOLECULES) is a CUDA code that enables large-scale, GPU-based MD simulations. The code of Fen Zi is now available in Google Code at http://code.google.com/p/fen-zi/. Any help or feedback is welcome!

Fen Zi currently includes: - NVT and NVE ensembles (NPT coming soon) - Force field: CHARMM force field, Flexible Water Models - Lennard-Jones interactions: Switching or shifting - Long distance electrostatic interactions: Ewald summation method and Reaction field - Solvent: Explicit or implicit model; TIP3; Flexible SPC/Fw water model - Exclusion lists for VDW and electrostatic interactions: NBXMod from 1 to 5 - Restraint potentials to probe the free energetic evaluation of processes - Shake/Rattle bond constraints for atom–atom bonds involving at least one hydrogen atom in the bonded pair

There is a listing of GPU accelerated scientific applications here.



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GPU-FS-kNN: A Software Tool for Fast and Scalable kNN Computation Using GPUs

A recent publication describes the development of a software tool GPU-FS-kNN (GPU-based Fast and Scalable k-Nearest Neighbour) for CUDA enabled GPUs. The basic approach is simple and adaptable to other available GPU architectures. They observed speed-ups of 50–60 times compared with CPU implementation on a well-known breast microarray study and its associated data sets.

The source code of the proposed GPU-based fast and scalable k nearest neighbor search technique (GPU-FS-kNN) is available at https://sourceforge.net/p/gpufsknn/ under GNU Public License (GPL).

There is a listing of GPU accelerated scientific applications here.



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Marvin Update

ChemAxon have just announced an update to Marvin the latest version is 5.11.5

Structures copied from ChemDraw or Accelrys Draw could not be pasted onto MarvinSketch has been fixed.



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Remote Printing

One of the advantages of the iPad and iPhone is I can travel to meetings or conferences with very little baggage and when I’m browsing poster sessions etc, I can just use a mobile device to take notes. Sometimes however I do need a hard copy for my records, whether it be notes from a lecture, a publication or even an invoice or receipt. I could save them all until I get back to the office but I prefer to print them out and have the hard copy waiting when I get back. To do this I use Dropbox and this Folder action.



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Chief Scientist to Steve Jobs

I didn’t know Richard Crandall (1947-2012) well but on the few occasions I did interact with him (most recently on graphics card processing in science) I was struck by his knowledge, enthusiasm and his willingness to go out of his way to help. Fortunately Stephen Wolfram did know Richard well and has written a fascinating blog entry that is well worth reading.



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MacMolPlt Updated

MacMolPlt is a cross-platform (Mac OS X, Linux and Windows) gui for preparing, submitting and visualizing input and output for the GAMESS quantum chemistry package. Features include a graphical molecule builder, GAMESS input generation, animation of output and visualization of molecules, normal modes, orbitals and other properties.

Surface

Version 7.4.4 update notes:

  • Fixed a seg fault when reading a single mode in a molplt file.
  • Fixed a bug related to fragement parsing.
  • Fixed a problem when deuterium was encountered. There is still not proper support for isotopes, but MacMolPlt should behave normally if they are encountered.
  • Modified MCSCF natural orbital parser for a recent change to GAMESS.
  • Added recent GAMESS coupled-cluster methods.
  • Added a parser for EOM-CC natural orbitals.
  • Added a parser for CAS-SCF diabatic molecular orbitals.
  • Cleaned up some potential 64 bit issues.



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Added ChemEquate to alphabetical listing

ChemEquate automatically formats and balances chemical equations. Copy with one click for use in word processing applications. Molecular weights are also conveniently provided.

FEATURES:

  • Create clear and professional looking chemical equations
  • Powerful tool for balancing chemical equations instantly
  • Export beautifully formatted equations to other applications
  • Quickly calculate the molecular weight of any compound
  • Save equations to Favorites list for future use


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Another clipboard manager

Cloud Clip allows sharing between Mac OSX and iOS and has an interesting duplicate detection feature. There is a Cloud clip helper which helps get around some of the sandbox issues. There is also a few clipboard sharing using email, Twitter etc.

I’ve added it to the page of clipboard managers.



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Cheminformatics workflows using mobile apps

Yet another publication describing the impact of mobile science.

We are perhaps at a turning point for making cheminformatics accessible to scientists that are not computational chemists. The proliferation of mobile devices has seen software or ‘apps’ developed that can be used for sophisticated chemistry applications. These apps can offer capabilities to the practicing chemist that are approaching those of conventional desktop-based software, while still apps tend to be focused on a relatively small range of tasks. Mobile apps that can pull in and integrate public content from many sources relating to molecules and data are also being developed. Apps for drug discovery are already evolving rapidly and are able to communicate with each other to create workflows, as well as perform more complex processes, enabling informatics aspects of drug discovery (i.e. accessing data, modeling and visualization) to be done anywhere by potentially anyone. We will describe how these cheminformatics apps can be used productively and some of the future opportunities that we predict.

There is a page of mobile science applications here.



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Green Solvents

Mobile science continues to make inroads, this publication describes the work to make Green Chemistry information more accessible.

Incorporating Green Chemistry Concepts into Mobile Chemistry Applications and Their Potential Uses DOI

There is a page of mobile science applications here.



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Script Debugger updated

Script Debugger 5.0.5 is a free maintenance release addressing a series of issues that came to light following the release of Script Debugger 5.0. This maintenance release improves compatibility with Mac OS X 10.8 by introducing support for bundle IDs in applets and droplets.

There are details of more Applescript tools in the Applescript Resources



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Dock Updated

DOCK is a suite of programs for molecular docking. In version 6.6 two new scoring functions are available: Grid-based footprint scoring and SASA-based scoring.

The MultiGrid Footprint Score calculates the pair-wise interaction energies over multiple grids.  Important receptor residues are initially identified with a reference ligand, and individual grids are generated to model such residues.

The SASA score calculates the percent exposure of a ligand, and the percentage of the hydrophobic portion of a ligand and the receptor that are buried in the pocket.

In addition, a symmetry corrected RMSD (Hungarian matching) method was added to facilitate pose reproduction studies.

Full information on what is new in DOCK 6.6



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CrystalMaker 8.7.1 released

CrystalMaker 8.7.1 has been released.

CrystalMaker is a program for building, displaying, manipulating and animating all kinds of crystal & molecular structures now with support for colour 3D graphics and multi structure animation.

crystalmaker

From the release Notes:-

  • Indexed Online Help. The online help system is now indexed. Users can search for terms in the Help menu's search box, and a list of appropriate topics is displayed in the menu.
  • Miscellaneous Changes. This version includes miscellaneous bug fixes and a workaround for system changes on OS X "Lion" and "Mountain Lion": Fixed a spurious "Failed to read XYZ file" warning that was displayed when a generic text file was read into the program. (The correct structure was invariably plotted, but the alert was incorrect). The Edit Annotation palette's "Scalebar" formatting buttons are now displayed correctly (this fixes an error introduced in the previous version). The Video Recorder palette now correctly resets the movie size to zero, before recording another video. Added a workaround for changed toolbar behaviour in OS X "Lion" and "Mountain Lion". Toolbar visibility is again correctly saved in the Preferences file. Fixed a potential problem with the File > Open Recent submenu, which could cause the command to fail.



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Restarting the lmgrd license server

I use Moe for molecular modeling work, this uses a license.dat file in each installed MOE root directory that must be updated with the contents that you have been given by CCG (either by hard copy or e-mail). You can use any ASCII text editor (I used BBEdit) to edit the file. The FlexLM license manager lmgrd must be configured and run. Usually this runs quietly in the background and needs little intervention, however I've found that on some occasions the server quits (perhaps after updates) and needs to be restarted. However since it is something I don't need to do regularly I always spend a while working out the exact syntax. So I created this short Applescript to restart the server. Each time MOE gets updated you need to change the folder path, and I’ve updated the details to reflect this.



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DataGraph 3.1 released

I just noticed that DataGraph has been upgraded to version 3.1

DataGraph is a simple and powerful graphing application for Mac OS X. It is a great companion for Excel, Numbers or any of the big statistical packages. Simple because it is very easy to draw plots, bar graphs, and fit functions. Start typing in data and the graph immediately shows up. Pick from the initial template list and modify the data, change colors, resize easily and interactively.

Included on the page of data analysis tools



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