Macs in Chemistry

Insanely Great Science

bioinformatics

New HELM web-editor

 

Just got this message..

The HELM project team is happy to announce the release of an open source web-editor to complement it's existing suite of software. This web-editor is designed to support organisations that do not wish to deploy a thick client. This is an initial release and the functionality will be extended in further releases during 2017.

HELM Web Editor brings HELM’s industry standard biomolecular representation to the browser, greatly enhancing the deployability of the technology for its adopters

Current functionality includes:

  • HELM 1 support
  • The ability to use the supplied monomer libraries to draw macromolecules, visualise them as sequences or atom/bond structures and calculate properties.
  • Import/export of HELM and xHELM.
  • A limited set of rules that allow you to manipulate the structure.

screenshot1


Comments

Scientific Applications under Sierra (Update 14)

 

Whilst there are many sites that track the compatibility on common desktop applications, it is often difficult to find out information about scientific applications. I’ll update the list regularly and feel free to send in information.

When I compiled a similar lists for Yosemite and El Capitan they proved very popular with 13,000 page views, I hope this page is similarly useful.

4Peaks no reported issues

Avogadro all seems OK

BBEdit version 11.6.2 and newer are compatible, recommend against using earlier versions

Brainsight requires version 2.3.3 for full compatibility with 10.12 Sierra. You could note too that 2.0 through 2.2.x will never work because 10.12 removed support for garbage collected applications. 2.3.x uses ARC

ChemDraw the official line is that it is not supported, even under El Capitan there were reports of copy/paste issues. One user reports “ChemDraw 15 is working fine for me. copy/paste, everything without issues”.

ChemDoodle no reported issues

CrystalMaker “We are pleased to confirm that all our latest software runs fine on macOS “Sierra”, as well as OS X 10.11 “El Capitan”, 10.10 “Yosemite”, and earlier.”

CYLview app launcher (icon on the desktop or the dock) does not work need to start using “Terminal”

DataDesk Data Desk 8 for Mac runs on OS X 10.7 up to 10.12

DataWarrior requires Java installation

DEVONagent has been updated to version 3.9.5 to support Sierra, in addition this update brings support for Qwant. DEVONthink has also been updated for Sierra.

EndNote From Endnote (Thomson Reuters) version 7: Message for Mac user planning to update to Sierra: In preparation for Apple's release of macOS Sierra on September 20, we have been testing various versions of EndNote. Through our testing, we discovered some issues with the EndNote PDF viewer. These issues have been reported to Apple, but in the meantime, we recommend that you DO NOT upgrade to macOS Sierra.

EnzymeX no reported issues

Evernote a bug in some versions of Evernote for Mac that can cause images and other attachments to be deleted from a note under specific conditions. We've released an updated version of Evernote for Mac, version 6.9.1, to resolve this.

Findings no reported issues

Fortran users will be happy to hear there are no reported issues with FTranProjectBuilder

GAMESS no reported issues.

Homebrew, after every update it is worth checking your homebrew installation.

Username$ brew doctor
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry and just ignore them. Thanks!

Warning: /usr/local is not writable.

You should probably change the ownership and permissions of /usr/local
back to your user account.
  sudo chown -R $(whoami) /usr/local

Warning: /usr/local is not writable.
Even if this directory was writable when you installed Homebrew, other
software may change permissions on this directory. For example, upgrading
to OS X El Capitan has been known to do this. Some versions of the
"InstantOn" component of Airfoil or running Cocktail cleanup/optimizations
are known to do this as well.

You should probably change the ownership and permissions of /usr/local
back to your user account.
sudo chown -R $(whoami) /usr/local

Once corrected you can then type

brew update
brew upgrade

You may get this error

$brew update
/usr/local/Library/brew.sh: line 32: /usr/local/Library/ENV/scm/git: No such file or directory

simply retyping brew update seems to resolve the issue

If you have previously installed Openbabel using

brew install mcs07/cheminformatics/open-babel --HEAD

The "--HEAD" part means install the latest development version from GitHub. The latest version of OpenBabel is now available so type

brew uninstall mcs07/cheminformatics/open-babel
Uninstalling /usr/local/Cellar/open-babel/HEAD... (309 files, 14.6M)
brew install mcs07/cheminformatics/open-babel

You can check you have the latest version installed by type this in a Terminal window

obabel -V
Open Babel 2.4.0 -- Sep 24 2016 -- 14:01:18

iBabel seems to work fine with the latest version of OpenBabel under Sierra. One advantage to updating to OpenBabel 2.4.0 is that previews now work with Quicklook.

quicklook

IDL does run under Sierra but does require some tuning. Detailed instructions here

iPython Notebook all working fine

Lego Mindstorms At the moment everything seems to be running really great on Sierra. However, please let you readers know they are welcome to contact us via the website way you did if they run into any errors. We'd be happy to solve them!

Manuscripts no reported issues

MarvinSketch I had to reinstall Java for Mac OSX this is the last version of Java Apple created to support legacy applications, similarly MarvinSpace and MarvinView.

Matlab in general appears to be fine except for certain language localisations these languages a patch is available for download. A patch is also available for MATLAB Runtime R2016b.

Mathematica 11.0.1 has been compatibility tested with macOS Sierra and you should not run into any OS-specific compatibility issues. The font-panel is disabled, but we are actively working to address this as soon as possible.

Mendeley no issues reported

MOE working fine, XQuartz did not need reinstalling. However the MOE app launcher (icon on the desktop or the dock) does not work because Apple changed some fundamental system components which affects lots of programs not specifically compiled for the newest MacOSXs. Also you cannot double click on a file to open it in MOE. You can still start MOE from the command line

Applications/moe2015/bin/MOE

It then works perfectly. Update, just had an email from CCG support, The problem with the MOE app launcher on MacOSX Sierra has been fixed in the MOE 2016 release.

MOPAC all seems to be working fine.

osra crashed with error abort trap: 6. I uninstalled using brew then reinstalled

brew uninstall osra
Uninstalling /usr/local/Cellar/osra/2.0.1... (7 files, 1.6M)
brew install osra

Then worked fine

Pandoc depends on llvm-3.5, not supported on Sierra. Llvm-3.9 is supported, installation using Homebrew seems to be OK.

Papers Mac 3.4.7 (527) is now available! Fixes a couple of problems under Sierra. A crash that can occur when switching PDFs, The search in PDF functionality is restored

R latest version (3.3.1) all seems fine

rdkit installed using home-brew works fine.

Readcube Version 2.22.13732 is Mac OS Sierra (v10.12) compatibility update.

Scansnap Note for using ScanSnap or ScanSnap Applications on macOS Sierra In order to avoid the ScanSnap compatibility problems, please do not use ScanSnap or ScanSnap applications on macOS Sierra in the following manner as doing so may cause some pages to be deleted or to become blank. Do not use [ScanSnap Organizer], [ScanSnap Merge Pages], or [CardMinder] Do not use Excellent mode when scanning A3 (11.7 in. x 16.5 in.) documents No image data will be lost nor any blank pages produced when content that has been scanned in the A4 (8.3 in. x 11.7 in.), Letter (8.5 in. x 11 in.), Legal (8.5 in. x 14 in.), or smaller sizes is saved.

Schrodinger a reader sent in this response. We received your query regarding MacOS Sierra. Unfortunately our current, 2016-3 release, do not yet support MacOS Sierra but we have plans to include support for this OS for the upcoming 2016-4 release of our software.

SeeSAR version 5.3 now, 5.4 will come out shortly. No compatibility issues observed/reported.

Studies no reported issues

UCSF Chimera version 1.11.1 seems to be working fine

Wizard worked great with the developer pre-releases, no reported issues

Vortex no problems so far, the embedded chemical drawing app Elemental appears to have no issues.

XQuartz did not require reinstallation :-) however there are reports of an intermittent display not found error when launching apps from a Linux box.

Allow applications downloaded from anywhere in macOS Sierra, if you open the security panel in the Settings the default options in Sierra are as shown below. There is no longer the option to open applications from Anywhere.

appstore

Apple have removed this function on macOS Sierra, but you can re-enable it running this in terminal

sudo spctl --master-disable

appstore2

You can restore it back to the default setting using

sudo spctl --master-enable

I’ll add more updates later.


Comments

Vortex does Biology

 

I was at the Dotmatics UGM recently and they gave an insight into some of the future directions. One of the areas under consideration is the use of Vortex support for Biological data analysis.

Vortex is a very high performance data analysis and plotting tool, capable of handling many millions of rows of data. It also has chemical intelligence built in, allowing structure-based searching, physicochemical properties calculation, clustering and match pair analysis.

The support for biology is a new addition and I've written a brief review here.

sequaligned

Added to the growing list of software reviews.


Comments

ICM version 3.8-5

 

MolSoft have announced the release of ICM version 3.8-5.

  • Generate a 2D Interaction Diagram of a ligand with the binding pocket. The image is annotated with hydrogen bonds and interacting residues.
  • 3D ligand editor is a powerful tool for the interactive design of new lead compounds in 3D
  • ICMJS is a JavaScript/HTML5 viewer for 3D Molecular Graphics which does not require any plugin or installation.
  • Support for MMTF format. The Macromolecular Transmission Format (MMTF)
  • Support for Mac retina display
  • Add docking restraints by selecting atoms in the receptor
  • Updates to protein modelling, bioinformatics and cheminformatics

Full release notes are here


Comments

BioExcel: An Introduction

 

An overview of the BioExcel Project.

BioExcel is based on improving three aspects of biomolecular research. Firstly, improving the performance and scalability of the most commonly used software, such as GROMACS (www.gromacs.org), HADDOCK (www.haddocking.org) and CPMD (www.cpmd.org), to take advantage of next-gen HPC systems and the expected increase in the amount of data produced. It’s also important to improve how easy it is for users to access and use these types of software. Not all researchers have experience in efficiently handling data and software. BioExcel aims to provide customisable workflow environments, which will allow relatively novice HPC/HTC users take advantage of the analysis software provided in ways that suit their specific research. In addition to this, hands-on training and public webinars are already underway, aiming to teach researchers best practices and how to best utilise the software and resources available.


Comments

Cytoscape Update

 

Cytoscape has been updated to version 3.4.0

Note, This update requires Java 8 is installed and Mac OS X 10.9 and later.

Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.


Comments

BALL Project

 

BALL (Biochemical ALgorithms Library) is an application framework implemented in C++ that has been specifically designed to reduce development times in the field of Computational Molecular Biology and Molecular Modeling. It provides an extensive set of data structures as well as classes for Molecular Mechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, and visualization.

BALLView is BALL’s standalone molecular modelling and visualization application. Furthermore, it is also a framework for developing molecular visualization functionality.

BALLView_01

It can be downloaded from here and requires

  • CMake >= 2.8.12
  • git
  • Python 2.7
  • Qt 5.4

Installation instructions for Mac OSX are here


Comments

Uniprot Feature Viewer

 

Data analysis tools are becoming ever more important as the volume of data increases and I thought I'd flag a new resource Feature viewer

A new visual approach by UniProt, the universal protein resource, presents protein sequence features in one compact view using a highly interactive BioJS component. This is the first visualisation feature in a public resource that lets users see different types of protein sequence features such as domains, sites, PTMs and natural variants from multiple sources in a single view.

featureviewer


Comments

HELM integration with RDKit

 

The Pistoia Alliance HELM project have announced free MarvinBeans 5.0 licenses and integration of HELM with the RDKit cheminformatics suite.

The Pistoia Alliance HELM project has made two major announcements that help cement the reputation of HELM as the de-facto standard for describing and working with complex macromolecular structures. Firstly, HELM users can now take advantage of free MarvinBeans 5.0 licenses for the HELM toolkit. Secondly, RDKit is now HELM-enabled, making it a valuable addition to the extensive range of open source HELM-enabled tools.

Comments

Protein-Ligand Interaction Profiler has been updated

 

The PLIP Protein-Ligand Interaction Profiler has been updated.

According to the Changelog

1.2.0

  • Support for DNA and RNA as ligands__
  • Detection of metal complexes with proteins/ligands, including prediction of geometry__
  • Extended result files with detailed information on binding site residues and unpaired atoms__
  • Support for zipped and gzipped files__
  • Rich verbose mode in command line with information on detected functional groups and interactions
  • Automatic fixing of common errors in custom PDB files
  • Refined binding site selection
  • Better overall performance
  • Initial test suite for metal coordination
  • Classification of ligands
  • Improves detection of aromatic rings and interactions involving aromatic rings
  • Single nucleotides and ions not excluded anymore as ligands
  • Generation of canonical smiles for complete (composite) ligands
  • Generation of txt files is now optional
  • Basic support for PDBQT files
  • Correct handling of negative chain positions of ligands
  • Improved check for valid PDB IDs
  • Fixes several bug

The web service includes all the updates and integrates BioLip for flagging biologically relevant interactions. Since ligand molecules (e.g., Glycerol, Ethylene glycol) are often used as additives (i.e., false positives) for solving the protein structures, not all ligands present in the PDB database are biologically relevant.

Comments

Polyphony

 

Polyphony is an open source software suite written in python. Its purpose is the superimposition free analysis and comparison of multiple 3D structures of the same or closely related protein molecules.

Absolute Requirements

python 2.6 or later, scipy, numpy, Biopython, especially the Bio.PDB module

Highly recommended

All following documentation assumes that you have these installed.

ipython , for interactive python scripting, matplotlib, for graph plotting, PyMOL, for interactive 3D visualisation. Open source version available on SourceForge

William R Pitt, Rinaldo W Montalvão and Tom L Blundell, BMC Bioinformatics, 2014, 15:324 doi

Comments

Workshop on Resources for Computational Drug Discovery

 

I just thought I'd mention this upcoming workshop, as ever there is a top class line up.

EMBL-EBI/Wellcome Trust Workshop on Resources for Computational Drug Discovery 2-6 November 2015 Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

https://registration.hinxton.wellcome.ac.uk/display_info.asp?id=510

The draft agenda is here

Comments

BioTuple Open Beta

 

iChemLabs the developers of ChemDoodle the very popular chemical drawing application have just announced the open beta of a new product BioTuple.

If you are looking for a bioinformatics system that encompasses all the aspects your workflow in one program, BioTuple™ is the solution for you. BioTuple works on all operating systems (both 32 and 64 bit), allows for easy importing and exporting to common biological file types, and keeps all the functions you would want organized into views. This allow you to easily switch between running an alignment, visualizing restriction sites and more in one cohesive interface

biotuplemainslider2

Objectives

  • Clean and clear graphics representations of sequences that are dynamic and responsive to keyboard and mouse input.
  • Quickly and easily import sequences from external databases such as NCBI and RCSB.
  • Visualization of features either manually or computer assisted for small and large sequences.
  • Highly customizable parameters for pairwise and multiple sequence alignments.
  • Alignment reports including phylogenetic trees, statistics, and consensus comparisons.
  • Clear visualization of all reading frames for RNA and DNA sequences.
  • Viewing of content analyses and properties of a given sequence.
  • Visualize the 3D structure of a sequence using PDB files imported from the RCSB.

As I mentioned this is an open beta and thus offers a unique opportunity to have an input into the design of the software, so please let your friends, colleagues and students know that this tool is available to them.

You can sign up for beta testing here: http://www.biotuple.com/beta-signup.


Comments

MacVector 14 released

 

A new version of MacVector has been released, the updated is now a 64-bit application meaning that it can take full advantage of all of the memory installed on your computer, allowing it to handle larger sequences and alignments. MacVector14 is no longer dependent on the deprecated “CarbonLib” compatibility library. This helps ensure that MacVector will continue to work with future releases of OS X where this library is likely to be removed.

Bowtie has been updated to support version 2 which can handle gaps in the aligned reads. This allows the use of much longer input reads (which typically have more indels) and provides far more accurate coverage information because, with the older version, reads with indel mismatches would be discarded even if they were "real" matches. The Primer Design (Primer3) “Test” mode now has a text output similar to the old Test PCR Primer Pair functionality, allowing you to view details of all of the possible products generated by the pair of primers. There are some cool new "Rounded Rectangle" feature graphics types. You can now directly select residues in the Map view in the default "zoom" mode. This lefts you use the Map tab for all editing operations except for actually typing residues (but you can select then click on the Editor tab to do that). MacVector now supports the new Regulatory GenBank feature type. You can import features into a sequence with files formatted using the Sequin Table format. More options in the way the sequence Editor and Map views are initialized are now saved to preferences so that MacVector “remembers” how you like to view your sequences. The cut sites and recognition sequences of restriction enzymes and now listed in the text outputs. Colored residues or background in the single sequence Editor tab are now only displayed if the underlying feature is located on the sequence line. This provides much finer control over which regions of the sequence you would like to see highlighted in color.

Comments

Protein-Ligand Interaction Profiler

 

Whilst this is not a Mac application I thought I'd mention it since it seems a very nice implementation.

The Protein-Ligand Interaction Profiler (PLIP) is a web service and command line tool for fully automated characterization of non-covalent interactions between proteins and ligands in 3D structures.

You can either upload a PDB format file or use the search facility to use a PDB by protein, ligand or enzyme-commission number. You can combine multiple search terms to be more specific (AND search).

I used the PDB code 3EQB, the software correctly identified two ligands, ATP and the more interesting ligand CHEMBL485945.

You can view the results using the embedded 3D molecule viewer JSmol shown in the image below.

plip1

PLIP is based on a python command-line application. In case you plan local mass/batch processing, you may want to use this one directly. The source code can be found on PLIP on Git Hub.

I first tried this out on my desktop machine and it worked beautifully, I then tried it out on my iPad and iPhone and the website functioned exactly as expected.

Comments

Unipro UGENE

 

I've just been sent details of a free open-source bioinformatics package Unipro UGENE first described in Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics 2012 28: 1166-1167. doi:10.1093/bioinformatics/bts091. Commercial support is also available.

3dstruct

Comments

Differ

 

Differ is an ultra-fast yet easy-to-use tool to browse, search, split and combine VCFs

Opening a 1.5 GB VCF file in a text editor can take a while, even on modern computers. Differ opens these VCFs in a second or two on any modern Mac (best with SSD).

Differ requires Mac OS X 10.10

Comments

Scientific Applications under Yosemite (Update 12)

 

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. I’ll update the list regularly and feel free to send in information.

I have a number of applications/libraries/toolkits installed using Homebrew and installed in usr/local, this is known to cause extended installation times for Yosemite. So don’t worry if it appears the install is stuck at 1 min remaining.

If you do use Homebrew then it is worth updating

brew update
brew upgrade

Aabel 3 appears to be working fine

BBEdit version 10.5.13 and newer are compatible with Yosemite

Beaker all seems OK

ChemBioDraw versions 12, 13 and 14 all function as before.

ChemDoodle all seems to work fine

Chimera aka UCSF Chimera versions 1.10 and higher are working on Yosemite.

Conquest and  Mercury from CCDC works fine but you may need to reinstall Quartz (see below)

Cresset report that after testing that Torch, Spark, Forge and Blaze appear to be compatible with Yosemite, the only cosmetic issues are due to a couple of as yet unresolved bugs in QT here.

Cytoscape 3.1.1 seems to be working fine

DataWarrior no issues

EndNote X7.2 works well with Yosemite.

Findings Electronic Notebook no issues, only small issue is that the ‘+’ button of the window does not trigger full-screen, though it can still be done via the Window menu.

IDL 8.2 and earlier gags on a missing reference in libPng.dyld, but IDL 8.3 and later is OK

Igor Pro version 6.3.5.5 works fine

iNMR no problems reported

MacVector 13.0.6 No significant issues reported

Marvin Marvin, Instant JChem, and JChem suite all work but require Java 7 (available here http://support.apple.com/kb/DL1572

Mathematica no issues reported

Matlab 2014b works fine, 2012a thru 2014a need patching (directions available from Mathworks support site. Older versions will not run at all..

MOE works fine but you may need to reinstall Quartz (see below)

OpenBabel no issues so far

Opsin all works fine

OSRA no issues

Papers Current version is compatible but not optimised, they hope to have a beta out of a substantially redesigned version next week.

Pro Fit 6.2 appears to work fine.

Pybel no issues reported

PyCharm works fine

Pymol All these are confirmed to work:

  • MacPyMOL 1.7.2.3
  • MacPyMOLX11Hybrid 1.7.2.3 after XQuartz reinstall (see below)
  • Open-Source PyMOL with homebrew

Known issues with MacPyMOL: - Movie export broken. Edu-only-PyMOL (free Student version) Does not work.(Now updated to work with Yosemite)
No reports so far about about - Other legacy versions (0.99 etc.) Apparently progam will not open - Open-Source PyMOL with fink or macports

PyRx 0.8 for docking works fine

RDkit no issues reported

SeeSAR all seems to be working fine

Sente 6.7.8 seems to run fine, except that it cannot open a reference library from the File > Open... dialog box. Workaround is to open from Finder.

Spartan 14 does not work because the Sentinel drivers are broken in Yosemite. The problem is NOT with Spartan, it is with the SafeNet developed Sentinel Run-Time Environment driver (the license manager). SafeNet has not given a definitive date when they will release an updated driver with Yosemite compatibility, but they are working on this. Best advice is to not upgrade but if you have to then contact support@wavefun.com for a temporary alternative license procedure.

Torch no issues

VarSeq no issues

Vortex Upgraded when the developer preview came out.  All works fine

The VVI products work well enough on Yosemite, but I'd like to achieve a higher level of quality for Yosemite (and iOS/iPad). There is an ongoing beta program for this product: https://itunes.apple.com/us/app/graph-ide/id904733611?mt=8 which is Graph Builder reincarnated on the iPad. There is also a beta program ramping for Graph Builder on Yosemite: https://itunes.apple.com/us/app/graph-builder/id470597599?mt=12 but a last minute interaction bug with Yosemite has delayed that for perhaps a few days. Please feel free to broadcast this information as you see fit. Beta program participation should be directed to support@vvi.com

VMD no issues reported

Wizard Pro is fully Yosemite compatible

XQuartz it seems the Yosemite installer deleted the symlink between /opt/X11 and /usr/X11; you can either reinstall Quartz or try "ln -s /opt/X11 /usr/X11"

Updated 30 October 2014

Comments

Biology Applications for MacOSX

 

I’ve been asked if I could include some biology/bioinformatics tools in the alphabetical listing, and I’m happy to add any that are sent to me, this week I’ve added.

CellDesigner

Cytoscape 3.1.1

GenomeBrowse

VarSeq

Comments

ConTour: Data-Driven Exploration of Multi-Relational Datasets for Drug Discovery

 

Caleydo is an open source visual analysis framework targeted at biomolecular data. It has been described in a number of publications and I noticed that a recent project ConTour included chemical structures.

Large scale data analysis is nowadays a crucial part of drug discovery. Biologists and chemists need to quickly explore and evaluate potentially effective yet safe compounds based on many datasets that are in relationship with each other. However, there is a is a lack of tools that support them in these processes. To remedy this, we developed ConTour, an interactive visual analytics technique that enables the exploration of these complex, multi-relational datasets.

Christian Partl, Alexander Lex, Marc Streit, Hendrik Strobelt, Anne-Mai Wassermann, Hanspeter Pfister, Dieter Schmalstieg ConTour: Data-Driven Exploration of Multi-Relational Datasets for Drug Discovery IEEE Transactions on Visualization and Computer Graphics (VAST '14), to appear, 2014.

I’ve added Caleydo to the listing of data analysis tools.

Comments

CLC Chemistry Workbench updated

 

The CLC Drug Discovery Workbench has been updated to version 1.5.

The new features are described on the updates page and in a video.

Comments

EnzymeX Updated

 

The Apple Design Award winning application EnzymeX has been updated. EnzymeX is a beautifully designed DNA sequence editor that Comes with numerous helpful tools and calculators, and includes handy reference data like codon tables and amino acid tables.

mapping

Talking to the developers they have fixed some 10.8/10.9 bugs, added gatekeeper support, and then reviewed the entire enzyme list and made quite a lot of changes as things had been updated throughout the years. In the process adding about 100 new enzymes, there is now Restriction enzyme information for almost 700 commercially available enzymes

Comments

Learning Python

 

It seems that Python is becoming the preferred language for scripting in science and I wrote a getting started page for Chemists and several people have pointed out a couple of resources that may be useful in particular Roaslind.

Rosalind is a platform for learning bioinformatics and programming through problem solving.

I looks like an excellent starting point for newcomers and more experienced programmers, whilst focussed on bioinformatics the exercises are useful for all disciplines.

For chemists chempython looks to be a very useful resource.

Comments

Chem-Path-Tracker

 

There is an interesting publication in the latest issue of Chemical Biology and Drug Design describing, Chem-Path-Tracker An automated tool to analyze chemical motifs in molecular structures DOI. This is a plugin for the molecular visualisation tool VMD that allows the user to highlight and reveal potential chemical motifs with a protein using only a few selections.

bindingsite

The chemical motifs can be a small group of residues or structure protein fragments with highly conserved properties that have important biological functions. However, the detection of chemical motifs is rather difficult because they often consist of a set of amino acid residues separated by long, variable regions, and they only come together to form a functional group when the protein is folded into its three dimensional structure. Furthermore, the assemblage of these residues is often dependent on non-covalent interactions among the constituent amino acids that are difficult to detect or visualize. To simplify the analysis of these chemical motifs and give access to a generalized use for all users, we developed Chem-Path-Tracker.

More details on the project page

Comments

RCSB mobile PDB viewer

 

The official PDB viewer has been updated

Comments

Amber 14 and Amber 14 Tools released

 

Version 14 of the Amber software suite has been released (There was no "unlucky" Amber13.)

  • Force fields: Amber has two new fixed-charge protein force fields, ff14SB and ff14ipq, a new modular lipid force field, Lipid14, and updates to nucleic acid and carbohydrate force fields.
  • Improved options for self-guided Langevin dynamics and accelerated molecular dynamics, to enchance sampling along soft degrees of freedom.
  • A completely reorganized Reference Manual
  • QM/MM calculations can interface with a variety of external quantum chemistry programs, expanding the types of quantum models available
  • More features from sander have been added to pmemd for both CPU and GPU platforms, including performance improvements, and support for extra points, multi-dimension replica exchange, a Monte Carlo barostat, ScaledMD, Jarzynski sampling, explicit solvent constant pH, GBSA, and hydrogen mass repartitioning. Support is also included for the latest Kepler, Titan and GTX7xx GPUs.
  • Expanded methods are available for free energy calculations that change Hamiltonian models, including better procedures for appearing and disappearing atoms, and tighter integration with replica-exchange simulations, and a new absolute free energy method.
  • New facilities are present for using electron density maps (e.g. from cryo EM/ET experiments) as constraints, and to support rigid (or partially flexible) groups in simulations.

Amber Tools have also been updated.

Among the new features in AmberTools14:

  • The sander module, our workhorse simulation program, is now a part of AmberTools;
  • Greatly expanded and improved cpptraj program for analyzing trajectories;
  • new documentation and tools for inspecting and modifying Amber parameter files;
  • Improved workflow for setting up and analyzing simulations;
  • new capability for semi-empirical Born-Oppenheimer molecular dynamics;
  • EMIL: a new absolute free energy method using TI;
  • New Free Energy Workflow (FEW) tool automates free energy calculations (LIE, TI, and MM/PBSA-type calculations);
  • Completely reorganized Reference Manual
Comments

GTKDynamo:- Molecular modeling extension for PyMOL

 

GTKDynamo is free/open source software which, together with pDynamo, transforms PyMOL into a powerful interface for molecular modeling. The interface has been designed to facilitate determining reaction pathways in biological systems, specially using hybrid QC/MM (or QM/MM) methods.

Some capabilities include:

  • Pure QC simulations - ab initio and SMO.
  • Pure MM simulations - using AMBER, CHARMM or OPLS force fields.
  • Hybrid QCMM simulations.
  • Single point calculations.
  • Energy minimization.
  • Molecular dynamics.
  • Reaction coordinate scanning.
  • Umbrella sampling.
  • Reaction path calculations - using NEB.

GTKDynamo is available for download for linux and Mac platforms . Please, make sure that you have installed:

  • pDynamo
  • Matplotlib
  • Numpy / Pylab
  • Pymol 1.x
  • pyGTK
  • ORCA, ab initio calculations.

GTKDynamo_overview-page001_800

J. F. R. Bachega, L. F. S. M. Timmers, L. Assirati, L. B. Bachega, M. J. Field, T. Wymore. J. Comput. Chem. 2013, 34, 2190-2196. DOI: http://dx.doi.org/10.1002/jcc.23346

Comments

PYMOL Updated

 

Whilst the update to PYMOL was announced as part of the Schrodinger update I thought it deserved a separate blog entry.

Graphics

  • Greater user control over color settings Color settings can be set as hexadecimal, colors, or floats ( [1., 1., 1.])
  • New ‘focalblur’ command
  • New ‘callouts’ for scene annotations

    Usability

  • Improved and extended Filter Wizard

  • New commands Retrieve bond properties with get_bond Load structures from PubChem by SID and CID codes with fetch
  • Improved PDB Loader graphical interface
  • Expanded documentation of settings
  • Access settings and properties from the iterate/alter commands via “s.” and “p.”
  • Improved labels to include customizable connectors to atoms, multiline labels, and more
  • Ability to select atoms by coordinates or by user-defined property
  • New selection keywords: metals, sidechain, backbone
  • CTRL-F to find objects or selections in the Object Menu Panel

    Bug Fixes

  • Dynamic measures now stored in session files

  • Sequence viewer colors fixed
  • Fixed inversion problem with ‘cealign’
  • Improved stability for shader-based rendering

    AxPyMOL

  • New option to embed content within a PowerPoint file

  • Support PowerPoint PPTX file format
  • Improved installer
  • AxPyMOL control displayed as an “Add In” on the PowerPoint Ribbon
  • 32-bit and 64-bit Office Support
  • Embeddable presentation content
  • Initial support for MAE files
  • Shader-based rendering support for volumes and improved graphics
  • Many bug fixes

The compiled PYMOL binaries are available for paid download with different options for academic, industrial and non-profit.

In addition the source code is available for free download. Not all new features make it to the source code right away, but eventually all features will, usually within a few months

Comments

Schrodinger Small Molecule Drug Discovery Suite Updated

 

The Schrodinger Small Molecule Drug Discovery Suite was updated over the weekend, this is a major update that brings in a host of new features and improvements.

Maestro Graphical Interface

Improved flexible ligand superposition Additional graphics settings
Real-time antialiasing Real-time ambient occlusion, outlines, and cartoon shading effects Multivariate ranking in the Project Table
Simultaneously maximize or minimize up to four property values, and rank entries based on the optimization Date Created and Date Modified fields automatically generated in the Project Table Workspace responsiveness of atom labels is up to 2.5x faster Click and drag to rearrange atom, measurement, and adjustment labels in the Workspace Support for bond labels Installed scripts and Tools menu items now searchable in the Task Tree Significant improvements to the Property Calculation interface in the project facility
Simultaneously calculate multiple properties Additional 2D properties now available: AlogP, #Hbond acceptors, #HBond donors, #rotatable bonds, polar surface area, molar refractivity, and polarizability

Ligand Docking

Ligand efficiencies are now calculated from the DockingScore instead of the GlideScore Generate per-residue interaction energies in Virtual Screening Workflow (VSW) for visualization New server mode in Glide Ligand Designer enables near real-time interactive docking (Glide Ligand Designer Script)

Pharmacophore Modeling

Performance improvements to Phase database operations, including faster deletion and insertion of ligands Automatic restart of Phase database subjobs

Field-Based QSAR

Use QM-calculated fields in 3D QSAR (command line only; phasefqsar script)
phase
fqsar script generates Jaguar input files for computing QM electrostatic fields for use in 3D QSAR

Molecular Dynamics

Monitor secondary structure elements over the course of the trajectory (Simulation Interactions Diagram; SID)

Quantum Mechanics

New interface to compute thermodynamic properties for reactions New faster TDDFT algorithm and graphical interface Compute Raman intensities Several improvements to the results script Jaguar pKa displays the computed pKa as an atom label by default Heat of formation graphical interface now supports bromine and iodine Improved numerical stability of the 1st and 2nd derivatives of the D3 correction Increased utility of canonical.py script
Script acts on a group of isomers and skips structures with unique stoichiometries

Protein X-Ray Refinement

Optionally set hydrogen B-values

Workflows & Pipelining

Includes the latest version of KNIME (v2.9)
Many new features including a Send Email node and ability to save workflows under different names; see http://tech.knime.org/whats-new-in-knime-29 for a complete list of new features Use any Glide simulation option in the Glide Ligand Docking node Employ a specific template in the Prime Build Homology Modeling node Import ungrouped structures to PyMOL from Run PyMOL node

Job Control

Improved fault tolerance Improved handling of suspended jobs in queueing systems

There are also updates to the Biologics Suite and the Materials Science Suite.

Comments

RELEASE OF CLC GENOMICS WORKBENCH 7

 

The new release comes with a long list of new features and improvements such as multi-sample RNA-Seq visualization, a completely new look and feel, and a new beta plugin with a memory-efficient read mapper. A few highlights from the release are:

  • A substantial update of the RNA-Seq Analysis tool
  • New statistical tools for analysis of differential expression
  • A number of new tools now being workflow enabled
  • Several new options for Workflows
  • Great improvements on speed and memory usage for copying data in the Navigation Area and between CLC Genomics Server and a Workbench
  • Complete redesign of the graphical user interface including new options for Side Panels and Views and a redesign of Zoom tools
Comments

Nebiocalculator from New England BioLabs

 

Nebiocalculator from New England BioLabs is actually web app using HTML5, javascript and CSS3, but it has been formatted for touch use so it works nicely on iPhones and iPads. Requires active internet connection.

  • molarity/dilution calculation
  • OD260 conversion
  • ligation calculation
  • mass/moles conversion for both dsDNA and ssRNA

photo

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

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

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

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

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

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

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



Comments

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



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

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

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

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.



Comments

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.



Comments

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



Comments

MacVector and ChemDoodle web components news

MacVector Inc have released a free version of MacVector.

If you used a temporary trial license, then when the 21 days were up, MacVector would simply refuse to start unless you entered a new valid license code. With the release of MacVector 12.7 we have changed that behavior. Now, when the trial license (or any annual license) expires, MacVector will give you the option of continuing to work, but with reduced functionality. All of the functions in the Analyze menu become disabled, but you can still open, edit, save and print MacVector documents, or save MacVector files in other formats.

ichemlabs have announced the release of ChemDoodle Web Components 5.

ChemDoodle Web Components 5 is a massive update. The most notable addition is a Full Sketcher, for drawing multiple molecules, shapes and figures, in addition to the Single Molecule Sketcher already provided. iChemLabs Cloud services and the ChemDoodle JSON format have been updated and drastically improved. The entire codebase has been reoptimized and cleaned, doubling the performance in desktop browsers and more than quadrupling the performance in mobile browsers. All Canvases now handle managing multiple molecules and shapes. Many new additions have been added and dozens of bug fixes have been implemented. We will be unrolling our new proprietary options over the next month, but of course, everything is available for free today under the GPL license!

There is a tutorial for using ChemDoodle web components here.



Comments

A Review of MOE 2012

I’ve just finished a review of the latest version of MOE from the Chemical Computing Group.

There are a number of new features that will be of particular interest to Mac users and I’ve included a few tips for using Marvin as the external 2D chemical drawing package.

system2

There is a collection of software reviews here.


Comments

Chemcomp release PSILO version 2012.11

The Chemical Computing Group have announced the release of PSILO version 2012.11. PSILO is a protein structure database and visualization system that provides an easily accessible, consolidated repository for macromolecular and protein-ligand information. Some key features in PSILO include:

  • 3D Interaction Query
  • Pocket Similarity Search
  • Project Standard Orientation

New and enhanced features in PSILO 2012.11 include: domain motif search, nonredundant BLAST summary report, automatic GPCR annotation and Interactive protein:ligand interaction diagrams. PSILO offers research organizations a means to systematically track, register and search both experimental and computational macromolecular data. A web-browser interface facilitates searching and accessing public and private data


Comments

MOE 2012.10 released

NEW & ENHANCED FEATURES IN MOE 2012.10

Integrated Protein Engineering Applications

  • Residue scanning to identify critical residues for affinity
  • Search for optimal mutations to modulate thermostability
  • Predict hydrophobic and electrostatic hot spots with the protein Patch Analyzer

Domain Motif Searching

  • Compare protein domains based on secondary structure elements
  • Search proteins for secondary structure sub-geometries
  • Identify similarities independent of sequence

Amber12:EHT: New Force Field for Biopolymers and Small Molecules

  • Amber12 parameters for proteins and nucleic acids
  • Extended Hückel Theory parameterization of small molecules
  • More precise treatment of resonance and substituent effects

Reaction-based Library Enumeration and Screening

  • New reaction engine combined with library enumeration or sampling
  • Sketch reactions or core/R-group libraries
  • Screen products with 2D or 3D filters (educts & products)

Usability Enhancements

  • Docked System Manager with control over surfaces
  • Undo, redo, keyboard shortcuts, configurable mouse, drag & drop, etc.
  • 2D sketcher integration with MOE Window

Comments

MacVector 12.7 is released

MacVector 12.7 is now available for download for all active users. Be sure to check out the new unique Cloning Clipboard window that simplifies creating new constructs

There is a new window available called the Cloning Clipboard that maintains a history of the DNA fragments created each time you use the Digest function. For example, if you select two restriction enzymes in a Map tab, then click on the Digest button, the fragment between the sites gets placed on the Cloning Clipboard. You can then join fragments together directly on the Cloning Clipboard by clicking on one end of a fragment and dragging to a different end

Comments

Molegro Virtual Docker

CLC bio is pleased to announce a new release of Molegro Virtual Docker , an integrated platform for computational drug design available for Windows, Linux, and Mac OS X. Molegro Virtual Docker offers high-quality protein-ligand docking based on novel optimization techniques combined with a user interface experience focusing on usability and productivity.

New features in version 5.5:

  • A new 'Energy Maps' tool provides volumetric visualization of protein force fields. This makes it possible to understand why a compound interacts with a given receptor, and may provide insights on how to improve the binding.

  • We also added a new execution mode in the Docking Wizard: 'Run Docking in Multiple Processes'. This makes it possible to run medium sized jobs on a local machine, while utilizing multiple CPU cores and even multiple GPU graphics cards. For large jobs on multiple machines, Molegro Virtual Grid should still be used.

  • The ray-tracer has been improved to more closely match the live 3D view output. This makes it possible to create high resolution renderings of the 3D view.

Comments

MolSoft updates

MolSoft have also released a new version of the free desktop molecular viewer ICM-Browser and the ActiveICM plugin  for viewing fully interactive molecules in web browsers.

Comments

A Quick Review of ChemBioDraw 13

This version of ChemBioDraw released in August 2012 is the first release since Cambridgesoft became part of Perkin-Elmer and there are a significant number of changes. This is the first version to be released since the introduction of Mac OS X 10.7 and 10.8 and both are now officially supported. In addition the ChemDraw plugin is now supported in 64 bit mode and Microsoft Office 2011 is supported. I’ve written a brief review here.

Comments

Viewing Docking results in Vortex using Astex Viewer

I recently wrote a review of ForgeV10 from Cresset in which I actually imported the results into Vortex to do the analysis. There were however two issues with doing this, firstly interpretation of the 3D structures is sometimes difficult, this can be resolved by creating a 2D rendering of the structure. The other issue is trying to interpret the docking pose whilst looking at the analysis of the results in say a Vortex scatter plot.

I’ve been working with Mike Hartshorn and the people at Dotmatics who have incorporated OpenAstexViewer (a 3D molecule viewer) into the application you can read the full article here..

Comments

Scripting Vortex 10

I’ve just added a new tutorial on scripting Vortex, starting to add user interaction.

Comments

Review of ForgeV10

This is a review of ForgeV10 the latest offering from Cresset, whilst a new product those familiar with FieldAlign and FieldTemplater will recognise much of the functionality. ForgeV10 allows the scientist to use Cresset’s proprietary electrostatic and physicochemical fields to align, score and compare diverse molecules. It allows the user to build field based pharmacophores to understand structure activity and then use the template to undertake a virtual screen to identify novel scaffolds.

There is a compilation of software reviews here.

Comments

PyMOL now on iPad

Schrodinger have just announced the release of PyMOL on the iPad. It is a free download from the App Store. With the app you can:-

  • View 3D molecular structures, images, and PDFs
  • Search and download data from the PDB, PubChem, Dropbox, or your own custom server.
  • Intuitively interactive: rotate, pan, twist, zoom, center, and adjust clipping planes, with simple gestures
  • Select atoms, residues, molecules, chains, objects, etc. – just by tapping the screen
  • Easy-to-use visualization presets cover the majority of visualization needs such as bond representations and surfaces.
  • Distance calculations, structure alignments, anaglyph 3D, and much more

photo

Comments

YASARA Updates

YASARA has seen several updates since I last mentioned it, most recently the ability to display pi-pi and cation-pi interactions.

ShowIntPiPi

YASARA is powered by PVL (Portable Vector Language), a new development framework that provides performance way above traditional software . PVL allows you to visualize even the largest proteins and enables true interactive real-time simulations with highly accurate force fields on standard computers. You can push and pull molecules around and work with dynamic models instead of static pictures.

Comments

Suggestions required

I just got this request,

Hi there, I was wondering if you knew of a program that offers similar functionality as Applied Maths BioNumerics software, but runs on Mac OS X (pref 10.7).

Not really my area, anyone have suggestions?

Comments

ChemDoodle web components updated

I just noticed ChemDoodle web components have been updated

This significant update improves performance and graphics for both 2D and 3D components. PDB file reading has been optimized on the Javascript side, and you can now control the resolution of protein and nucleic meshes, leading to significantly faster loading. Two new spectrum components have been added, OverlayCanvas which draws several spectra in the same domain, and SeekerCanvas which shows plot coordinate information.

You might want to have a look at this review and this tutorial

Comments

MacVector 12.6 released

MacVector 12.6 is now available for download

MacVector is a comprehensive Macintosh application that provides sequence editing, primer design, internet database searching, protein analysis, sequence confirmation, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, and a variety of other functions.

The release notes gives full details of the update

Comments

FITTED Suite 3.6 released

FITTED is a suite of programs to dock flexible ligands into flexible proteins. This software relies on a genetic algorithm to account for flexibility of the two molecules and location of water molecules, and on a novel application of a switching function to retain or displace water molecules and to form potential covalent bonds (covalent docking) with the protein side-chains.

The Suite includes many new features and implementations:

FITTED is a suite of programs (FITTED, PREPARE, ProCESS and SMART), JAVA GUI for easy keyword file editing and docking, Fully automated and flexible protein docking program, Automated covalent docking, Automatic protein preparation from pdb to mol2, Multi-mol2 support for docking and ligand processing, Uses an evolutionary algorithm, Semi-flexible protein docking with flexible waters, Has the ability to consider water molecules displaceable, Keyword files are simpler than ever, Support for Windows, Linux 32 and 64 bits, Mac OSX.

Comments

New Additions to alphabetical listings

Added to alphabetical listing

ARP/wARP is a software project for automated protein model building and structure refinement. It is based on a unified approach to the structure solution process. It combines electron density interpretation using the concept of the hybrid model, pattern recognition in an electron density map and maximum likelihood model parameter refinement with REFMAC.

The REFMAC program can carry out rigid body, tls, restrained or unrestrained refinement against Xray data, or idealisation of a macromolecular structure. It minimises the coordinate parameters to satisfy either a Maximum Likelihood or Least Squares residual. There are options to use different minimization methods. (At the moment only CGMAT is active.) REFMAC also produces an MTZ output file containing weighted coefficients for SigmaA weighted mFo-DFcalc and 2mFo-DFcalc maps, where "missing data" have been restored.

Toxtree is a full-featured and flexible user-friendly open source application, which is able to estimate toxic hazard by applying a decision tree approach. Toxtree could be applied to datasets from various compatible file types. User-defined molecular structures are also supported - they could be entered by SMILES, or by using the built-in 2D structure diagram editor.

Comments

MyGenome app for iPad

It has now been a couple of years since the human genome was first sequenced and we are now seeing companies offering personal genome sequencing. Illumina are now offering MyGenome an iPad app that allows you to explore a real human genome. In due course they hope to allow you to explore your own genome.

There is more information about the app here.

Now added to the mobile science page.

Comments

ByoDyn a python tool for biological simulations

In systems biology it is becoming a routine task to build models of increasing complexity on a given biochemical network or pathway of interest. One of the main problems in building such models is the determination of the parameters underlying each modelled process. ByoDyn has been designed to provide an easily extendable computational framework to estimate and analyse parameters in highly uncharacterised models

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Graphite - LifeExplorer

Just added to the alphabetical listing

Graphite - LifeExplorer is a tool for modelling DNA, the tool generates DNA along a Bézier curve, open or closed, allows fine-tuning of atoms' position and, most importantly, exports to PDB. This software allows to model in 3D assemblies of proteins and DNA. Its main feature is the capability to create 3D models of DNA in a highly intuitive manner. To date, the modeling and visualization tool allows to: - import PDB files - create isosurface of molecular object - highlight residues of interest - calculate distance between residues pairs - import and export in 3D formats - model DNA and export the result in PDB - visualize a 3D scene with Level of Detail - explore a scene with real-time ambient occlusion - import a file with x,y,z coordinates and convert it into a DNA representation.

You can see a it in action here

http://www.youtube.com/watch?feature=player_embedded&v=9db1hXZARoo

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AMBER 12 released

A new version of AMBER 12 and AMBER Tools 12 has been released, the main changes are:-

  • Force fields: Amber has a new fixed-charge protein force field, ff12SB, enchanced support for polarizable potentials and a new modular lipid force field Lipid11 designed to be compatible with the other pairwise additive AMBER force fields.
  • Expanded options for numerical Poisson-Boltzmann solvation calculations, including models for membrane systems and support for periodic systems.
  • An enchanced 3D-RISM integral equation model, using the Kovalenko-Hirata (and other) closure approximations, with a better treatement of aqueous electrolytes.
  • Improved ideas for self-guided Langevin dynamics and accelerated molecular dynamics, to enchance sampling along soft degrees of freedom.
  • Simplified installation and automatic update support.
  • Semi-empirical quantum calculations can use d-orbitals, allowing the use of Hamiltonian models such as AM1/d and PM6.
  • QM/MM calculations can interface with a variety of external quantum chemistry programs, expanding the types of quantum models available.
  • More features from sander have been added to the pmemd code for both CPU and GPU, including Temperature Replica Exchange, Isotropic Periodic Sum, Accelerated Molecular Dynamics and support for various harmonic restraints based on the use of NMRopt on GPUs.
  • Expanded methods are available for free energy calculations that change Hamiltonian models, including better procedures for appearing and disappearing atoms, and tighter integration with replica-exchange simulations.
  • New facilities are present for using electron density maps (e.g. from cryo EM/ET experiments) as constraints, and to support rigid (or partially flexible) groups in simulations.

There are detailed instructions for installing AMBER 12 under MacOSX and building CUDA enabled AMBER 12.

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ICM Update

MolSoft have announced the release of ICM version 3.7-2c.

New features include Atomic Property Fields APF is a 3D pharmacophoric potential implemented on a grid. APF can be generated from one or multiple ligands and seven properties are assigned from empiric physico-chemical components (hydrogen bond donors, acceptors, Sp2 hybridization, lipophilicity, size, electropositive/negative and charge).

The 3D ligand Editor is a powerful new tool for the interactive design of new lead compounds in 3D. It allows you to make modifications to the ligand and see the affect of the modification on the ligand binding energy and interaction with the receptor.

Use AQUASITES to design chemicals based on their ability to displace or keep water molecules inside the ligand binding site of proteins. The first step is to identify water binding sites and then the second step is to estimate the free energy of water displacement for a particular ligand(s).

Protein Modelling Inside ICM there are many features for homology modelling and loop modelling. This new option can be used if you have a gap in your protein and you want to find loops in the PDB which fit the gap.

"Pipe-able" Scripting in ICM. New options to pipe icm commands and scripts. Easy way to write pipe-able scripts (see $ICMHOME/molpipe/*.icm). Easy way to add parallelism to unix/mac ICM scripts: fork with pipe option ($ICMHOME\molpipe*.icm)

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Added JTreeView to data analysis tools

JTreeView renders gene expression data into several interactive views.

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EBioTools 3

There have been a few comments about an older blog posting concerning EBioTools so I thought I’d bump it to the top of the list.

EBioTools is a compilation of bioinformatics software that has been packaged for easy installation on Mac OS X. It covers many areas, from simple sequence analysis to RNA folding and sequence assembly.

The included software is:

  • Name Version
  • Boost1.3.41
  • Clustal W1.83.UNIX
  • PHYLIP3.6b
  • EMBOSS5.0.0
  • EMBOSS.kaptain0.98
  • gd2.0.35
  • Glimmer3.02
  • HMMER2.3.2
  • INFERNAL0.7
  • Jmol11.2.12
  • Kalign2
  • Kaptain0.72
  • MrBayes3.1.2
  • MRSr482
  • MUSCLE3.6
  • NCBI Tools2.2.16
  • NEdit5.5
  • Primer31.1.2
  • sim42003-09-21
  • soap4r1.5.8
  • Staden1.7.0
  • T-COFFEE5.05
  • ViennaRNA1.6.5

As mentioned in the comments added to the older post “EBioTools works under Snow Leopard and Lion but Staden is broken because Apple changed several Libraries to make the MacOSX core "smaller". Most issues are due to Apple changing graphic libraries.”

Users might also be interested in eBioX which brings easy-to-use sequence analysis to Mac-using biologists. It features an editor for sequences and multiple alignments, and graphical viewers for trace files and molecule structures. Many popular file formats are supported. Databases can be created locally or queried over the network, both for metadata and homology (BLAST). Analysis functions include searching for patterns, primers, restriction sites and repeats, translation and back translation, calculating DNA melting temperature, dot plots, as well as aligning sequences (multiple, local and global). Multiple alignments can be created by several of the most popular algorithms

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ViennaRNA Updated

I was just catching up with some reading and I came across an article in Algorithms for molecular biology describing ViennaRNA 2.0 consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. With the new release of version 2.0, they introduce the most recent nearest neighbour energy model for all free energy calculations. Additionally, most of the stand-alone programs included are now able to read FASTA formatted input data. The distribution includes:-

  • RNAfold -- predict minimum energy secondary structures and pair probabilities
  • RNAeval -- evaluate energy of RNA secondary structures
  • RNAheat -- calculate the specific heat (melting curve) of an RNA sequence
  • RNAinverse -- inverse fold (design) sequences with predefined structure
  • RNAdistance -- compare secondary structures
  • RNApdist -- compare base pair probabilities
  • RNAsubopt -- complete suboptimal folding
  • RNAplot -- RNA structure drawings in PostScript, SVG, or GML
  • RNAcofold -- predict hybrid structure of two sequences
  • RNAduplex -- predict possible hybridization sites between two sequences
  • RNAup -- predict RNA-RNA interaction sites using accessibilities
  • RNAalifold -- predict the consensus structure of several aligned sequences
  • RNAaliduplex -- comparative (multiple alignment) version of RNAduplex
  • RNALfold -- predict locally stable structure of long sequences
  • RNAplfold -- compute average pair probabilities for local base pairs in long sequences
  • RNApaln -- fast structural alignment of RNA sequences using string alignments
  • Several small but helpful Perl Utilities

According to the authors both 1.8.x and 2.0 versions of the Vienna package compile and run on Mac OS X. Currently there's a small compile problem with the included Perl module and the latest gcc versions on Intel based Macs. The defaults for gcc recently changed to compile only Intel code, while the installed Perl is a fat binary containing both PPC and Intel code. The download page contains instruction how to work around this by simply setting an environment variable.

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MacVector Updated

I just got a note that MacVector has been updated to version 12.5 MacVector is a comprehensive Macintosh application that provides sequence editing, primer design, internet database searching, protein analysis, sequence confirmation, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, and a variety of other functions. MacVector is widely regarded as the most intuitive, easy to use program available for sequence analysis.



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XplorSeq

XplorSeq is a software package that facilitates the compilation, management and phylogenetic analysis of DNA sequences Read More...
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eBioTools

How to get eBioTools to run. Read More...
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CLC Workbench

Update to the CLC bioinformatics workbenches. Read More...
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