SAMSON is a novel software platform for computational nanoscience. Rapidly build models of nanotubes, proteins, and complex nanosystems. Run interactive simulations to simulate chemical reactions, bend graphene sheets, (un)fold proteins. SAMSON's generic architecture makes it suitable for material science, life science, physics, electronics, chemistry, and even education. SAMSON is developed by the NANO-D group at INRIA, and means "Software for Adaptive Modeling and Simulation Of Nanosystems.
SAMSON has an open architecture which allows anyone to extend it - and adapt it to their needs - by downloading SAMSON Elements (modules). SAMSON Elements come in many flavors: apps, editors, controllers, models, parsers, etc., and are adapted to different application domains. SAMSON Elements help users build new models, perform calculations, run interactive or offline simulations, visualize and interpret results, and more. Add new SAMSON Elements to SAMSON straight from SAMSON Connect.
In the latest news Python scripting is coming to SAMSON 0.7.0. Most of the SAMSON API is now exposed in Python, and this will allow you to create models and run simulations, generate movies, perform analysis and reporting, etc., directly from scripts. Python will make it even easier to integrate and pipeline SAMSON and SAMSON Elements with well-known packages from diverse fields, e.g. TensorFlow, PyRosetta, RDKit, ASE, etc., to name a few
SeeSAR 7.1 has just been released.
- 3D-pharmacophores to identify compounds of interest By now, you can run so many bulk actions, your solution list will grow by the minute. This made it just the right time to implement another filter option to help you keep track! Pharmacophore filters can now be defined using so-called sphere constraints. You can apply these pharmacophores at lightning speed to the molecule table and drill down solutions sets quickly and effectively with queries such as: Which molecules have an acceptor at this position? Filter out molecules that occupy this position! Give me all molecules with an aromatic moiety here!
- Linking and merging fragments with the integrated ReCore It is now possible to enter the 3D molecule editor with more than just one molecule. Among other things, this facilitates linking and merging operations with ReCore. Simply select the atoms you seek to replace (eg the terminal atoms of two fragment binders that should be linked). A click on the ReCore button retrieves for you in seconds fragments that link the two binders, leaving them as closely as possible in place.
- Better measure and label-options (with adjustable font size) Partially hidden labels in 3D won't bother you anymore! Instead, the simple labels for showing distances, angles, and so on have been upgraded to the more advanced labels which we have always used for Hyde and more recently for displaying torsion information. These labels are movable (simply click and drag) and are always at the front. Plus, as a bonus feature, you may now also adjust the font size on the labels in the appearance settings menu in the toolbar.
- Parallel high-throughput docking A lot of users have been waiting for this feature! Now bulk docking can be carried out with just one click. Plus we have parallelized the docking calculation so that it now uses all processors on your computer, providing you with solutions swiftly — just as your hardware permits.
- Multiple selections for bulk actions Frankly speaking we previously "abused" the favorite icon for making selections to initiate bulk actions. This itself undermined the point of being able to mark molecules as favorites. Now you may conveniently select multiple molecules using the new check box feature, and initiate bulk actions on the basis of this selection. For your convenience we also added a few functions to make working with these selections even more effective (un/check all, invert, ...). Just as for the favorites, shift + left mouse click works on the check boxes as a multiple un/check feature.
BBEdit everyone's favourite text editor has been updated. This looks to be a substantial update with over 100 new features and refinements, the full release notes are available here.
A couple of features look very useful
There's a new submenu on the Edit menu, "Columns". This submenu contains commands to help you work more easily with column-delimited text files. The three basic commands, "Cut Columns", "Copy Columns", and "Clear Columns" work similarly to their top-level analogues. The columns to be cut/copy/cleared are determined by the selection range: to cut a single column, for example, click in the middle of it. You can cut/copy/clear multiple columns by selecting text across them. The "Rearrange Columns" command gives you an easy way to, well, rearrange the columns in a column-delimited text document. Choose the menu command, and then drag the items into the list to order them as you would like, then press the "Apply" button.
There's a new command on the Text menu: "Canonize". This command is useful for doing batch search-and-replace operations in a file, using another file as a list of search-and-replace transformations.
BBEdit 12.0 requires macOS 10.11.6 ("El Capitan") or later, and is compatible with macOS 10.13 "High Sierra". I've added it to the list of Scientific Applications under High Sierra
According to the data captured by mixpanel three weeks after launch iOS 11 has overtaken iOS 10. This is important information for developers who can start to focus on the latest version of the mobile operating system.
In contrast for Android there is a much larger spread of operating systems in use.
A couple of apps have been updated recently.
Wolfram|Alpha across thousands of domains--with more continually added--Wolfram|Alpha uses its vast collection of algorithms and data to compute answers and generate reports for you. Always one of the top apps on the MobileSciencesite.
ChemistryKeyboard is a specialized Keyboard Extension for anyone who needs to enter chemical formulae. This update brings:
- Improved layout for wider iPads including tab button and less intrusive labels
- Added arrow types
- More elements keys on wide displays
- Keyboard in the Chemistry Keyboard app was not showing localization
Elemental from Dotmatics the FREE Chemistry Sketch Utility now supports iOS 11 (64-bit support).
R Instructor now version 2.1.4 with core code rewritten.
NEB Tools brings New England Biolabs’ most popular web tools to your iPhone. Use Enzyme Finder to select a restriction enzyme by category or recognition sequence, or search by name to find information on any NEB enzyme.
iSpartan includes viewing NMR data from iSpartan 16.
Findings electronic lab notebook.
I just came across a new Electronic LabNotebook (ELN), eLabFTW is an open source solution powered by PHP/MySQL in Docker containers. One install can be for a team, or the whole institution. You can also install it on your computer for a personal notebook.
All the user needs is a web browser to access the notebook.
Upload any type of files, embed images in the text, Draw doodles directly with your mouse, Use templates for your experiments, Draw molecules with Chemdoodle, REST API for accessing programmatically your experiments, SAML2 authentication if you have an identity provider, Growing community of users and contributors scrutinizing the code and improving it, Highly customizable: you can change the colors, the status list, the items types list, etc. Can fit any kind of lab (chemistry, biology, physics, astronomy, etc.)
There is also a demo account available https://demo.elabftw.net.
ChemDraw is a very established chemical drawing package that probably set the standard for publication quality chemical drawing. However, on the Mac platform in particular I think it is true to say Cambridgesoft have taken their eye off the ball and released versions that were not up to their usual standard.
ChemDraw 17 is in someways a fresh beginning you can read the full review here.
Booking Reminder! The 3rd Tony Kent Strix Annual Lecture - FREE Event - Friday October 20th 2017
In 2016 the UK eInformation Group (UKeiG), in partnership with the International Society for Knowledge Organisation UK (ISKO UK), the Royal Society of Chemistry Chemical Information and Computer Applications Group (RSC CICAG) and the British Computer Society Information Retrieval Specialist Group (BCS IRSG) was delighted to announce that the winner of the prestigious Tony Kent Strix Award was Maristella Agosti, Professor in Computer Science, Department of Information Engineering at the University of Padua, Italy. The Award is given in recognition of an outstanding practical innovation or achievement in the field of information retrieval.
Professor Agosti has built a world-wide reputation for her work in many aspects of information retrieval and digital libraries. She was one of the first people to work in information retrieval in Italy where she acted as a catalyst for creating a vibrant and internationally recognised IR research community.
Her 2017 Strix Lecture will be given at The Geological Society, Burlington House, Piccadilly, London during the afternoon of Friday 20th October.
The 2017 Tony Kent Strix Award winner will also be announced during the afternoon.
* This is a FREE event, open to everyone, BUT advance bookings ARE required. Please book your place by emailing Gary Horrocks at: firstname.lastname@example.org *
Full programme details:
2.00 Doug Veal - Chairman's welcome
2.10 - A presentation from Alan Gilchrist
Title: 'Reflections: Some thoughts on the past, present and future of Information Retrieval'
(Doug and Alan are founding members of the Working Group that initiated the Award, first presented in 1998.)
2.45 - Questions & Discussion
3.00 - Tea & coffee
3.45 Maristella Agosti - The Tony Kent Strix Annual Memorial Lecture
Title: Behind the Scenes of Research and Innovation
Abstract: We often excel in producing scientific achievements, but at times turning those achievements into innovation and technology transfer can be a tall order. Furthermore, even though we may document our findings well in scientific publications and reports, we are far less accomplished and proficient in documenting and explaining how the complex process of transforming scientific results into innovation has been performed and proven successful. In general, most of the knowledge of this transfer process remains only with those taking part in it, while certain aspects such as the time and context when the transfer took place may be rich in lessons to be learnt and provide opportunities for future teaching in diverse fields. This talk addresses the complex process of transforming research outcomes into innovation using some relevant examples in the fields of information retrieval and digital libraries.
4.30 Questions & discussion
5.00 Meeting closes
The Annual Lecture series is sponsored by Google.
For more information about UKeiG and the Tony Kent Strix Award visit:
ChemTube3D is a web based Open Educational Resource containing interactive 3D animations and structures, with supporting information for some of the most important topics covered during an undergraduate chemistry degree. It was developed by the ChemTube3D team including students at the University of Liverpool.
This is an absolutely fantastic resource that offers invaluable insight into the 3D structure of molecules and reactions.
I'm delighted to hear that it is now accessible from a mobile device
There are many more science apps listed on the Mobile Science site.
Pharmacelera we have written a python script to generate conformations with RDKit and made it available here .
Conformer generation is one of the first and most important steps in most ligand based experiments, particularly when the ligand’s 3D structure is unknown. For example, the quality of the conformers could affect the results of virtual screening experiments.
I just saw this message on the rdkit mailing list and I thought I'd flag it.
I've noticed a problem with anaconda python on the Mac. This may also be a problem on linux, but I haven't tested that yet.
Due to some changes in the way the anaconda team is doing python builds, the most recent conda python builds seem to no longer work with the RDKit. The symptom is an error message like "Fatal Python error: PyThreadState_Get: no current thread" when you try to import the rdkit.
I've observed this for the newest 3.5 (3.5.4-hf91e95415) and 3.6 (3.6.2-hd0bf7f115) builds. A workaround is to downgrade to 3.5.3 (conda install python=3.5.3) or 3.6.1 (conda install python=3.6.1).
Whilst there are many sites that track the compatibility on common desktop applications, it is often difficult to find out information about scientific applications. Based on the number of page views on the lists for Sierra, El Capitan and Yosemite it is apparently a useful resource. The major change with High Sierra is the update to the file system so hopefully this will be a benign update, but a Time Machine backup is always a good idea.
I’ll update the list regularly and feel free to send in information.
High Sierra is a major download 5GB and a couple of people have asked if it is possible to keep the installer and then use it on multiple machines.
The initial installer is small (15 MB) but after the main installer has successfully downloaded (5GB+), when you are prompted to start the installation process, click Cancel, and the installer will be in the /Applications folder. You must make a copy of this to another location; otherwise if you launch the installer and it completes the High Sierra update, it'll be deleted.
When you upgrade to macOS High Sierra, systems with all flash storage configurations are converted automatically. Systems with hard disk drives (HDD) and Fusion drives won't be converted to APFS. You can't opt-out of the transition to APFS.
AppleScriptObjC there are a couple of bugs, because the issues stem from the .bridgesupport file, they will potentially pose problems in other languages that use the scripting bridge.
Avogadro no issues
BBEdit have a comprehensive list of compatibility notes for each application and versions https://www.barebones.com/support/new-os.html. BBEdit 12 has just been released which bring full High Sierra compatibility.
ChemDoodle all seems fine no issues reported
ChemDoodle3D all seems fine no issues reported
ChemDraw as a policy they do not test until after new operating systems have been released, will check back later
ChirysView no issues to date
Cresset No issues to date, more detailed testing underway.
CrystalMaker no problems
DataWarrior no issues to date
iBabel no issues to date
MarvinSketch latest version no issues, earlier versions may require the old Apple supplied JDK to be reinstalled
MarvinView no issues
Microsoft have already announced the results of preliminary testing of the Office suite.
Office version 15.35 and later, Word, Excel, PowerPoint, Outlook, and OneNote will install and run on 10.13, but there maybe some issues
Office 15.34 and earlier. These versions are not supported on 10.13. In some cases, you may not be able to launch the Office apps.
Office for Mac 2011. Word, Excel, PowerPoint, Outlook and Lync have not been tested on macOS 10.13 High Sierra, and no formal support for this configuration will be provided.
Mnova lite no issues reported
MOE There seem to be no problems running MOE 2016.0804 or higher on MacOS 10.13.
Please note that all of our Mac users should upgrade to MOE 2016.0804 due to bugs identified in earlier versions. You can download the patch to 2016.0804 http://www.chemcomp.com/support/12/moebin_2016.0804.tgz
The default python is
~ /usr/bin/python Python 2.7.10 (default, Jul 15 2017, 17:16:57) [GCC 4.2.1 Compatible Apple LLVM 9.0.0 (clang-900.0.31)] on darwin Type "help", "copyright", "credits" or "license" for more information.
PyCharm no issues
StarDrop Our initial tests suggest that everything is working as expected.
Vortex no issues reported.
Updated 14 October 2017
A web-based chemistry ELN using the OpenBabel toolkit published recently https://doi.org/10.1186/s13321-017-0240-0DOI
The web based application is available as an Open Source software that offers modern solutions for chemical researchers. The Chemotion ELN is equipped with the basic functionalities necessary for the acquisition and processing of chemical data, in particular the work with molecular structures and calculations based on molecular properties. The ELN supports planning, description, storage, and management for the routine work of organic chemists. It also provides tools for communicating and sharing the recorded research data among colleagues. Meeting the requirements of a state of the art research infrastructure, the ELN allows the search for molecules and reactions not only within the user’s data but also in conventional external sources as provided by SciFinder and PubChem.
Project home page: https://github.com/ComPlat/chemotion_ELN
Developed/tested on Linux and Mac, deployed on Linux.
Just catching up on reading the literature and came across this interesting python paper in Journal of Cheminformatics. DOI.
Scoria is useful for both analyzing molecular dynamics (MD) trajectories and molecular modeling. For example, we have used beta-version Scoria functions to create large-scale lipid-bilayer models, to construct small-molecules models with improved predicted binding affinities, to measure MD-sampled binding-pocket shapes and volumes , and to develop neural-network docking scoring functions, among other applications. As an additional example, in this manuscript we describe a trajectory-analysis Scoria script that colors the atoms of one protein chain by the frequency of their contacts with a second chain.
The popular molecular visualisation application Pymol has been updated to version 2.0. This is a major update and the changes are detailed below.
You can either download a disk image (117 MB) or instal using Anaconda (Python 2.7)
conda install -c schrodinger pymol
- Unified modern interface
- PyQt interface replaces Tcl/Tk and MacPyMOL on all platforms
- Anaconda Python distribution
- Better third-party plugin and custom scripting support
- Open access incentive executables with new licensing mechanism
- Native retina resolution / 4k display support
- Dock/undock and rearrange certain panels (Builder, Feedback Browser, Volume Editor)
- Support for trackpad gestures (pinch for zoom in/out, z-rotate)
- Dedicated dialogs for opening MAE files, MTZ files, maps and trajectory files
- New APBS Plugin panel
- .pymolrc script editor with syntax highlighting
- Properties editor
- Improved Draw / RayTrace dialog
- MPEG-4 and GIF movie export panel
- Excel exporter plugin (Windows and Mac)
- Open files by dragging from file browser to PyMOL window
- wire and licorice representation aliases for combined lines/nonbonded and sticks/nb_spheres
- New commands: “copy_to” and “uniquify”
- Single-letter code labels (“label oneletter”)
- Label Wizard menus for colors and transparency
- Improved file types registration on Windows (Setting > Register File Extensions)
- Changed default values for several settings:
- autoshowclassified=1 (=3 for > 500k atoms)
- “Open Recent” file menu
- File > New Window opens new PyMOL window
- Setting > Register File Extensions
- Plugin > Legacy Plugins
- New > Pseudoatom > Callout
- A > Copy to object
- A > State > Split
- Fixed slow performance of “extract” command
- Better unicode/UTF-8 handling
- Fixed inconsistent look of labels and connectors on Retina and non-Retina displays
- Fixed labelrelativemode=2 raytracing
- Improved Maestro and MOE format compatibility
- Fixed internal GUI clipping on certain Windows systems with integrated Intel graphics
The new user interface and all core improvements will be pushed to the open source SVN repository early next year.
It is really useful to have two sites of metabolism tools available that use contrasting methodologies, FAME 2 using curated dataset of experimentally determined metabolism data to build a machine learning model using simple descriptors. In contrast SMARTCyp uses precomputed activation energies from density functional theory (DFT) calculations of model compounds.
I previously wrote a script displaying the [results of a SMARTCyp calculation in a webview. The first part of the script imports the smartcyp.jar, however with each update I was finding issues so I thought it might be better to simply treat SMARTCyp as a command line application and use subprocess to access it.
Using a similar script we can also access FAME2
The new version of Xcode is available for download. Xcode 9.0 includes Swift 4 and SDKs for iOS 11, watchOS 4, tvOS 11 and macOS High Sierra 10.13.
- The source code editor has been completely rebuilt for amazing speed. It scrolls at a constantly smooth rate, no matter the files size, also supports Markdown.
- Refactoring to easily select and modify structure of code
- Swift 4 compiler can also compile Swift 3 to aid transition
- Xcode 9 makes working with source control – and with GitHub – easier and more tightly integrated.
- Simulator app updated.
Chemfp is a set of command-line tools and a Python library for working with cheminformatics fingerprints. It can use OEChem/OEGraphSim, RDKit, or Open Babel to create fingerprints in the FPS format, and it implements a high-speed Tanimoto search.
The software is available under the MIT license. For more information see http://chemfp.com/. Documentation is available from http://chemfp.readthedocs.io/en/chemfp-1.3/ .
There are many changes over chemfp 1.1, which was the last release of the public/no-cost version of chemfp. The biggest ones are:
Tested against the current version of all of the toolkits
Added support for the Avalon and pattern fingerprints in RDKit
In-memory Tanimoto searches for 166-bit MACCS keys on computers with the POPCNT instruction is about 30% faster.
FPS loading is about 40% faster. As a result, file-based searches are about 25% faster.
The in-memory search algorithms in version 1.1 were parallelized with OpenMP, but the NxM k-nearest search was left out. That case is now also parallelized.
Some of the APIs from the commercial version were backported to 1.3, including the fingerprint writer API and functions for substructure fingerprint screening.
Added and improved docstrings
This release support Python 2.7 but it no longer supports Python 2.5 or Python 2.6. The commercial version supports Python 2.7 and Python 3.5+, handles more than 4GB of fingerprint data, and has a binary fingerprint format for fast loading.
It is available from http://dalkescientific.com/releases/chemfp-1.3.tar.gz.
Molecular dynamics simulation in general, and GROMACS in particular, has made it possible to study large and complex biomolecular systems such as membranes and membrane proteins and probe atomic detail that is not accessible to any experimental methods. GROMACS can already use thousands of cores and hundreds of accelerators efficiently in parallel, even for a single quite small system. When adding ensemble-level parallelization with Copernicus the total problem scaling extends another two orders of magnitude.
These release notes document the changes that have taken place in GROMACS since version 2016.3 to fix known issues. It also incorporates all fixes made in version 5.1.4 and several since.
- Fixes where mdrun could behave incorrectly
- Disabled PME tuning with the group scheme
- Fixed value of Ewald shift
- Fixed orientation restraint reference
- Fixed bugs with setup for orientation restraints
- Worked around missing OpenMP implementation in orientation restraints
- Enable group-scheme SIMD kernels on recent AVX extensions
- Fix FEP state with rerun
- Fixed COM pull force with SD
- Fix PBC bugs in the swap code
- Fixed flat-bottomed position restraints with multiple ranks
- Fixed null pointer print in DD
- Improved the “files not present” error message
- Fixed LJ-PME + switch grompp error
- Fixed unused SIMD PME table kernel
- Fixed bugs in most double-precision Simd4 implementations
- Avoid inf in SIMD double sqrt()
- Fix NVML error messages
- Fixed IMD interface malfunctions
- Fixed initial temperature reporting
- Fix exception in SIMD LJ PME solve
- Fixes for gmx tools
- Fixed memory access issues in gmx solvate
- Fixed a consistency check in gmx make_edi for flooding
- Supported quiet trajectory-handling I/O
- Improved documentation
- Migrated much content from the wiki to the user guide
- Corrected the PDF manual to reflect that all tools are called gmx
- Clarified gmx editconf help text
- Added missing .mdp file documentation for the enforced rotation module
- Fixed parameter description for dihedral_restraints
- Replaced instance of “group” by “coord” in pull .mdp documentation
- Portability enhancements
- Supported CUDA 9/Volta for nonbonded kernels
- Really enabled AVX512 in the GROMACS-managed build of FFTW
- Fixed aspects for compiling and running on Solaris
- Fixed AVX512F compiler flags
- Fixed compiler flags for using MKL
- Fixes compilation issues with ARM SIMD
SeeSAR is a software tool for interactive, visual compound prioritization as well as compound evolution. Structure-based design work ideally supports a multi-parameter optimization to maximize the likelihood of success, rather than affinity alone. Having the relevant parameters at hand in combination with real-time visual computer assistance in 3D is one of the strengths of SeeSAR.
This update includes
- Full integration of ReCore functionality. Now - besides fragment-replacement, joining and merging of fragments is also possible. In addition, you can fine-tune results delivered by ReCore using pharmacophore filters.
- Editing turns into full-blown designing. Besides atom by atom changes you may now add the most common rings with just one klick. So large changes can quickly be made to molecules and this in itself necessitates another new feature — namely that multiple poses are generated based on a superposition of the maximum common substructure.
- Display of torsion distribution. On the one hand, we have now integrated the latest update of the database of torsion angle distributions from the CSD, while on the other, it is now possible to view the torsion angle distribution for a particular rotatable bond.
- Miscellaneous enhancements. The SDF export covers your particular selection of favourites and any comments attached to a molecule. For a numerical filter it is now possible to define both a lower and upper bound. Last but not least, besides distances, you may now measure angles and torsions.
An interesting blog post
The aim of this blog post is to highlight some of the key features of the KNIME Deeplearning4J (DL4J) integration, and help newcomers to either Deep Learning or KNIME to be able to take their first steps with Deep Learning in KNIME Analytics Platform.
I've become a great fan of Jupyter Notebooks as a way of modelling cheminformatics data, and I've published some of the notebooks here.
The Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations, visualizations and explanatory text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, machine learning and much more.
In the predicting AMES activity notebook I also looked at the use of pickle to store the predictive model and then access it using a Jupyter notebook without the need to rebuild the model. Whilst a notebook is a nice way to access the predictive model it might also be useful to be able to access it from other applications or from the command line.
In this tutorial we look at providing command line access to the model and then incorporating it into a Vortex script.
FAME DOI is a collection of random forest models trained on a comprehensive and highly diverse data set of 20,000 small molecules annotated with their experimentally determined sites of metabolism taken from multiple species (rat, dog and human) designed to predict sites of metabolism. FAME 2 DOI builds on this work to improve accuracy ,in addition FAME 2 uses a slightly modified version of the visualization developed by Patrik Rydberg and implemented in SMARTCyp using ChemDoodle Web Components.
An interesting development for those working in nano materials.
We have completed the development of IM-UFF (Interactive Modeling - UFF), an extension of UFF that combines the possibility to significantly modify molecular structures (as with reactive force fields) with a broad diversity of supported systems thanks to the universality of UFF. Such an extension lets the user easily build and edit molecular systems interactively while being guided by physically-based inter-atomic forces. This approach introduces weighted atom types and weighted bonds, used to update topologies and atom parameterizations at every time step of a simulation. IM-UFF has been evaluated on a large set of benchmarks and is proposed as a self-contained implementation integrated in a new module for the SAMSON software platform for computational nanoscience.
This contribution has been submitted to the Journal of Molecular Modeling.
SAMSON is a novel software platform for computational nanoscience. Rapidly build models of nanotubes, proteins, and complex nanosystems. Run interactive simulations to simulate chemical reactions, bend graphene sheets, (un)fold proteins. SAMSON’s generic architecture makes it suitable for material science, life science, physics, electronics, chemistry, and even education. SAMSON is developed by the NANO-D group at INRIA, and means “Software for Adaptive Modeling and Simulation Of Nanosystems”.
I've written a couple of docking/virtual screening workflows using SMINA, a freely available tool DOI. There are a number of other alternatives and it is very difficult to get good comparisons which is why the Grand Challenges are useful.
The Grand Challenge 3 (GC3) is a blinded prediction challenge for the computational chemistry community, with components addressing pose-prediction, affinity ranking, and free energy calculations. GC3 is based on six different protein targets, Cathepsin S and five different kinases, and is separated into five subchallenges, some of which involve multiple protein targets. Only Cathepsin S is associated with cocrystal structures, so the kinase components of this challenge focus on affinity ranking and/or free energy predictions. Three of the datasets, Cathepsin S, JAK2 and TIE2, include a free energy prediction component.
This is an ideal opportunity to test novel algorithms on a carefully curated dataset.
Computational practices often employ a number of computational algorithms and dataset preparation steps for meaningful results. D3R will provide a forum for deposition, dissemination and discussion of such workflows through this website. Workflows will represent methods used successfully in the blinded challenges and methods donated by our pharmaceutical and/or academic collaborators. GitHub.
In Stage 1 September 1 - October 1, your predicted poses for the 24 ligands, in a coordinate system aligned with the S04-bound Cathepsin S structure provided in the inputs. Your predicted affinities, or affinity rankings, for all 136 compounds and/or your predicted absolute or relative binding affinities (in kcal/mol) for the free energy subset of 33 compounds. When Stage 1 closes, we will release the crystallographic poses of the 24 ligands.
In Stage 2 October 1 - December 1, your predictions of the affinity rankings of all 136 compounds and/or absolute or relative binding affinities (in kcal/mol) for the free energy subset of 33 compounds.
Apple have announced a major new update of Mac OS X, version 10.13 High Sierra has a number of significant changes and it is likely that applications may need to be updated. Beta test versions of the operating system have been available for a while now and the more proactive developers have already been testing their software. Unfortunately there will always be developers who seem to refuse to test their applications until the new Mac OS has been officially released.
Microsoft have already announced the results of preliminary testing of the Office suite.
Office version 15.35 and later, Word, Excel, PowerPoint, Outlook, and OneNote will install and run on 10.13, but there maybe some issues
Office 15.34 and earlier. These versions are not supported on 10.13. In some cases, you may not be able to launch the Office apps.
Office for Mac 2011. Word, Excel, PowerPoint, Outlook and Lync have not been tested on macOS 10.13 High Sierra, and no formal support for this configuration will be provided.
I'm in the process of updating the Jupyter notebooks to Python3 and I looking at what I can do make sure other people can reproduce the results. At the moment I annotate the imported python modules with version numbers in the Jupyter notebook. Finding the versions is a bit tedious and I was wondering if there was some way to automate this?
from rdkit import Chem #rdkit 2016.03.5 from rdkit.Chem import PandasTools import pandas as pd #pandas==0.17.1 import pandas_ml as pdml #pandas-ml==0.4.0 from rdkit.Chem import AllChem, DataStructs import numpy #numpy==1.12.0 from sklearn.model_selection import train_test_split #scikit-learn==0.18.1 import subprocess from StringIO import StringIO import pickle import os %matplotlib inline
Apple have updated the online support documentation to give more details about the new file system (APFS) that is coming with the next generation of the operating system High Sierra. Apple File System (APFS), is the default file system in macOS High Sierra for Mac computers with all flash storage, it is designed to scale from an Apple watch to a Mac Pro.
Apple File System is a new, modern file system for iOS, macOS, tvOS, and watchOS. It is optimized for Flash/SSD storage and features strong encryption, copy-on-write metadata, space sharing, cloning for files and directories, snapshots, fast directory sizing, atomic safe-save primitives, and improved file system fundamentals. APFS replaces HFS+ as the default file system for iOS 10.3 and later, and macOS High Sierra and later.
A few things that might be important to note.
- When you upgrade to macOS High Sierra, systems with all flash storage configurations are converted automatically. Systems with hard disk drives (HDD) and Fusion drives won't be converted to APFS. You can't opt-out of the transition to APFS.
- FileVault volumes are converted from HFS+ to APFS, just like unencrypted volumes.
- Devices formatted as HFS+ can be read and written to by devices formatted as APFS.
- Devices formatted as APFS can be read and written to by any APFS-formatted devices but only by HFS+ formatted devices running macOS 10.12.6 or later.
- Volumes formatted with APFS can't offer share points over the network using AFP. SMB and NFS are supported when using APFS. The option to enforce only SMB-encrypted share points is also available.
What are the advantages?
- APFS supports 64-bit inode numbers, supporting over 9 quintillion files on a single volume
- APFS is optimized for SSD storage, it will work with traditional hard disk drives as well.
- No need to repartition, APFS allows Space Sharing, which lets multiple file systems share the same underlying free space on a physical volume rather than use a fixed amount of space for each file system.
- APFS supports sparse files, extended file attributes and TRIM operations, as well as using a copy-on-write metadata scheme to ensure that updates to the file system are crash-safe.
- Apple File System supports encryption natively, both single key encryption and multi-key encryption (where each file is encrypted with a separate key, and metadata is encrypted with a different key).
It is almost certain that any third party disc utilities will need to be updated. Once upgraded to APFS the only way to return to HFS+ is to erase the disc losing all data.
APFS implements normalization and case insensitivity according to the Unicode 9.0 standard; this enables APFS to support a wider range of languages for these features than HFS+, which is based on Unicode 3.2. However beta testers report issues with languages that include non-Roman characters. Hopefully this will be addressed soon.
I notice that DataWarrior has had a couple of updates recently.
DataWarrior combines dynamic graphical views and interactive row filtering with chemical intelligence. Scatter plots, box plots, bar charts and pie charts not only visualize numerical or category data, but also show trends of multiple scaffolds or compound substitution patterns.
The latest updates
v04.06.01: August 2017
Fixed plugin interface bug. Various small bug-fixes and improvements.
v04.06.00: July 2017 new plugin interface to easily develop database access extentions
DataWarrior can be downloaded here http://www.openmolecules.org/datawarrior/download.html.
This looks interesting Molecular Query Language (MolQL) a declarative language for describing selections/substructures of molecular data. The language provides a wide range of queries and can be used as a compilation target for various selection expressions such as the ones provided by PyMol, JMOL, or VMD.
There are a number of examples that you can explore in your web browser here.
This guide is a set of Jupyter notebooks intended to help researchers already familiar with molecular dynamics simulation learn how to use OpenMM in their research and software projects.
# For Mac OS X, substitute `MacOSX` for `Linux` below wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh bash -b ./Miniconda3-latest-Linux-x86_64.sh -p $HOME/miniconda export PATH=$HOME/miniconda/bin:$PATH conda install --yes -c omnia -c conda-forge jupyter notebook openmm mdtraj nglview
There is a detailed document describing OpenMM here
OpenMM is a set of libraries that lets programmers easily add molecular simulation features to their programs, and an “application layer” that exposes those features to end users who just want to run simulations. Instructions for installation under MacOSX are here.
OpenMM works on Mac OS X 10.7 or later. OpenCL is supported on OS X 10.10.3 or later.
I use BBEdit for Markdown Editing, in fact I use BBEdit for just about any text based manipulating, script editing etc. and I regard as an essential "swiss army knife" for my computer.
I know lots of people use TextWrangler but I understand that this is no longer being supported.
We are sunsetting TextWrangler, and we encourage anyone interested in TextWrangler to download and use BBEdit instead.
They also provide a handy chart showing the differences.
If however you only require a Markdown Editor there are plenty to choose from.
First let me say I’m not a big Fortran user but any blog posts about Fortran always seem to be very popular, and I do get asked regularly about how to compile Fortran applications.
So I've decided to gather together all the Fortran news, tips and resources onto a dedicated Fortran on a Mac page.
If you know of anything else it would be useful to include please let me know.
A very useful paper https://arxiv.org/abs/1708.05070
Here we contribute a thorough analysis of 13 state-of-the-art, commonly used machine learning algorithms on a set of 165 publicly available classification problems in order to provide data-driven algorithm recommendations to current researchers. We present a number of statistical and visual comparisons of algorithm performance and quantify the effect of model selection and algorithm tuning for each algorithm and dataset. The analysis culminates in the recommendation of five algorithms with hyperparameters that maximize classifier performance across the tested problems, as well as general guidelines for applying machine learning to supervised classification problems.
Good to see my preferred method Random Forest close to the top of the ranking based on performance over 165 datasets.
The rankings show the strength of ensemble-based tree algorithms in generating accurate models: The first, second, and fourth-ranked algorithms belong to this class of algorithms.
All 13 ML algorithms were used as implemented in scikit-learn, a popular ML library implemented in Python.
One of the great features of the latest version of Vortex (> build 29622) is the ability to script multiple sub-structure searches using SMARTS. There are many occasions when this sort of feature is useful, if you want to flag molecules that contain reactive functional groups, toxicophores, or PAINS functional groups that have been shown to interfere with high-throughput screens. Vortex tutorial 24 described how to do this multi-substructure searching.
There have now been a couple of new publications describing the identification of false positives in high-throughput screening campaigns in which the binding of glutathione S-transferase (GST) to glutathione (GSH) is used for detection of GST-tagged proteins.
- Identification of Small-Molecule Frequent Hitters of Glutathione S-Transferase–Glutathione Interaction DOI
- Identification of Small-Molecule Frequent Hitters from AlphaScreen High-Throughput Screens DOI
There have also been some suggestions as to how some of the motifs might be interfering with the assay, as shown below.
I've now added the additional structural motif definitions taking the total to 550 SMARTS definitions. It is perhaps worth mentioning that some of these motifs may not be an issue when using alternative screening technologies, but it may be very worthwhile to double check any molecules flagged by this script before committing significant resources to follow up.
This comment in Nature is perhaps worth noting
Academic researchers, drawn into drug discovery without appropriate guidance, are doing muddled science. When biologists identify a protein that contributes to disease, they hunt for chemical compounds that bind to the protein and affect its activity. A typical assay screens many thousands of chemicals. ‘Hits’ become tools for studying the disease, as well as starting points in the hunt for treatments. These molecules — pan-assay interference compounds, or PAINS — have defined structures, covering several classes of compound. But biologists and inexperienced chemists rarely recognize them. Instead, such compounds are reported as having promising activity against a wide variety of proteins. Time and research money are consequently wasted in attempts to optimize the activity of these compounds. Chemists make multiple analogues of apparent hits hoping to improve the ‘fit’ between protein and compound. Meanwhile, true hits with real potential are neglected.
I've updated the tutorial and the scripts for download.
In the previous workflow I described docking a set of ligands with known activity into a target protein, in this workflow we will be using a set of ligands from the ZINC dataset searching for novel ligands. Once docked the workflow moves on to finding vendors and selecting subsets for purchase.
Whilst I've seen lots of examples of printed small models this is the first time I've seen an example of models suitable for using as teaching aids in a lecture theatre, excellent idea.
Three-Dimensional Printing of a Scalable Molecular Model and Orbital Kit for Organic Chemistry Teaching and Learning DOI
Three-dimensional (3D) chemical models are a well-established learning tool used to enhance the understanding of chemical structures by converting two-dimensional paper or screen outputs into realistic three-dimensional objects. While commercial atom model kits are readily available, there is a surprising lack of large molecular and orbital models that could be used in large spaces. As part of a program investigating the utility of 3D printing in teaching, a modular size-adjustable molecular model and orbital kit was developed and produced using 3D printing and was used to enhance the teaching of stereochemistry, isomerism, hybridization, and orbitals.
The 2017 Summer Newsletter is now available for download.
This includes reports from the scientific meetings supported, and details of potential future meetings, together with news items that might be of interest to members of RSC CICAG interest group.
The Chemical Information and Computer Applications Group (CICAG) is one of the RSC’s many member-led Interest Groups.
The aims of the group are:-
- support users of chemical information, data and computer applications and advance excellence in the chemical sciences
- inform RSC members and others of the latest developments in these rapidly evolving areas;
- promote the wider recognition of excellence in chemical information and computer applications at this level.
If you are an RSC member who is interested in joining the group contact the membership team
I've just written a review of the latest version of ChemDoodle3D
ChemDoodle 3D is a scientific visualization platform with a focus on user customizability and universal support. Just like its 2D counterpart, all of the graphics are fully customizable and controllable. The large feature set is well organized for intuitive access and we develop ChemDoodle 3D to work with the vast majority of graphics cards in use.
ChemDoodle3D really excels at the creation of high quality publication ready graphics, the ability to specifically select every atom or bond enables the user to precisely create the desired image. It performs well using modest hardware that would be accessible to any student. Perhaps one of the real attractions however is the ability to use the ChemDoodle Web Components to easily share structures via the web.
The Khronos™ Group, an open consortium of leading hardware and software companies, announced at the SIGGRAPH 2017 Conference the immediate public availability of the OpenGL® 4.6 specification. OpenGL 4.6 integrates the functionality of numerous ARB and EXT extensions created by Khronos members AMD, Intel, and NVIDIA into core, including the capability to ingest SPIR-V™ shaders.
The OpenGL 4.6 specification can be found at https://khronos.org/registry/OpenGL/index_gl.php. The GLSL to SPIR-V compiler glslang has been updated with GLSL 4.60 support, and can be found at https://github.com/KhronosGroup/glslang.
Just had a look at the Mobile Science Website the top five upvoted apps are:-
ChemDoodle Mobile Draw, 3D, Calculate, Spectra for molecules
Medicinal Chemistry Toolkit Cheng-Prusoff; Dose to man; Gibbs free energy to binding constant; Maximum absorbable dose calculator; Potency shift due to plasma protein binding
Wolfram Alpha Wolfram|Alpha uses its vast collection of algorithms and data to compute answers and generate reports for you.
Findings- Lab Notebook With Findings, your lab notebook is always with you and always up to date, be it on the field, at the bench, or at a conference.
Elemental Elemental from Dotmatics the FREE Chemistry Sketch Utility
I have updated the page showing the interactive plots using Flot and ChemDoodle Web Components
iMolView has been updated.
iMolview lets you browse and view in 3D protein and DNA structures from Protein Data Bank, and drug molecules from DrugBank. Search for drug names like 'ibuprofen' or 'gefitinib' in DrugBank, or proteins like 'insulin' or 'thyroid receptor' in PDB. Information associated with each molecule in these databases is also at your fingertips. Sync and view your own structure files via iTunes. Molecular view can be customized with a rich set of molecular representations (wires, balls-and-sticks, space filling, ribbon diagrams, molecular surfaces) and various coloring schemes.
What's New in Version 1.9.1
- Fixed number of compatibility issues with modern iOS versions and devices
- Added retina support for all devices
- Added support for new PDB online directory
- Added support for new Electron Density Map server
- Fixed crash with some large PDB files.
- Minor UI changes
I previously mentioned a comparison of various tools to cluster large datasets. I've now updated the Vortex to allow the user to select the centroid of each cluster. I tried it on a 4.3 million structure clustered dataset and the script only took a few seconds to run.
The page on clustering is here and the Vortex script can be downloaded here http://macinchem.org/reviews/vortex_scripts/ChoseCentreFromClusters.vpy.zip.
SeeSAR 6.1 has been released, looking at the release notes there are a couple of useful additions.
- Multiple protein alignment, Since version 5.6 it has been possible to load and work with multiple proteins. So far this feature could only be utilized with pre-aligned structures. Now you can do the 3D alignment in SeeSAR itself. The alignment is based on and optimized according to the superposition of related active sites. Therefore, once you have selected a binding site, just one click is all that is needed to superpose all related binding sites at once. Note that the superposition is limited to highly homologous proteins (>90% sequence identity).
- SeeSAR/StarDrop interface. We have implemented a new function that greatly improves the interaction between the two software packages. Using the option in the molecule table toolbar, you may now transfer all (or the subset of favorite) molecules directly to StarDrop, which is launched automatically. This interface is supported in StarDrop starting with the recently released StarDrop version 6.4 and StarDrop now analogously supports launching and submitting data to SeeSAR. So it is in fact possible to transfer data back and forth and exploiting maximum synergy to make the best of both worlds. Note that this feature may require a few adjustments in your SeeSAR settings to become fully functional.
- Shortcut to copy protein ligands. Usually among the first tasks after loading proteins is to copy the related protein ligands to the molecules table for further processing (docking, editing, re-scaffolding, etc.). Especially with multiple proteins this turned out to be a quite cumbersome procedure. Therefore we have implemented a shortcut function in the toolbar of the proteins tab to copy all protein ligands at once to the molecules table. Note that this function will copy all ligands irrespective of their position in relation to the common binding site that is used in the context of the molecules table. So some of the copied ligands may lie well outside the common binding site.
SeeSAR is a software tool for interactive, visual compound prioritization as well as compound evolution. Structure-based design work ideally supports a multi-parameter optimization to maximize the likelihood of success, rather than affinity alone. Having the relevant parameters at hand in combination with real-time visual computer assistance in 3D is one of the strengths of SeeSAR.
- New Date & Time integration
- Integration with the H2O machine learning library
- KNIME Personal Productivity now part of KNIME Analytics Platform
- Wrapped metanode composite view
- A new version of the Python integration
- Logistic Regression nodes are more scalable, faster, and support regularization
- Audio and speech recognition nodes
- New Cloud Connectors
Whilst high-throughput screening (HTS) has been the starting point for many successful drug discovery programs the cost of screening, the lack of access to a large diverse sample collection, or the low throughput of the primary assay may preclude HTS as a starting point and identification of a smaller selection of compounds with a higher probability of being a hit may be desired. Directed or Virtual screening is a computational technique used in drug discovery research designed to identify potential hits for evaluation in primary assays. It involves the rapid in silico assessment of large libraries of chemical structures in order to identify those structures that most likely to be active against a drug target. The in silico screen can be based on known ligand similarity or based on docking ligands into the desired binding site.
I've updated the description to give more information about preparing the target protein.
Chirality-2 has been released, this is a game that aims to teach some fundamental concepts in 1st year University level organic chemistry in a fun and innovative way, using drag and drop and touch based interfaces to solve puzzles and answer questions.
ChemSearch has been updated to enhance searching of the Acros catalogue
The Chemistry Keyboard is a specialised Keyboard Extension for anyone who needs to enter chemical formulae. The update improves stability on large screen iPads.
The new version (2.5.0) of Gabedit has been released and is available for download at http://gabedit.sourceforge.net/
Gabedit is a graphical user interface to computational chemistry packages like Gamess-US, Gaussian, Molcas, Molpro, MPQC, OpenMopac, Orca, PCGamess and Q-Chem. It can display a variety of calculation results including support for most major molecular file formats. The advanced "Molecule Builder" allows to rapidly sketch in molecules and examine them in 3D. Graphics can be exported to various formats, including animations.
Here is a list of the significant changes between 2.5.0 and 2.4.8:
- Minor bugs fixed.
New tools for VASP :
- read geometries (Optimization or M. Dynamic) from VASP OUTCAR file
- read geometry from VASP POSCAR file
- Create VASP POSCAR file
Read dielectric function from a VASP xml file and compute optic properties : the refractive index n(w), the extinction coefficient k(w), the absorption coefficient alpha(w), the reflectivity R(w), the energy loss spectrum L(w), and the optical conductivity sigma(w).
- read data from vasprun.xml and plot DOS, pDOS and, Bands structures
- Gabedit can now read the hessian from .hess orca file. After reading of the hessian, Gabedit computes frequencies, modes and effective masses.
- Export in CChemI : update
- Tv accepted (used by Gaussian and Mopac for periodic system). Using Tv, Gabedit can generate other cells.
- deMon2k is now supported (Thanks to Dennis Salahub, Mauricio Chagas da Silva, Jonathan Kung and Morteza Chehelamirani for their suggestions, corrections, comments,...)
- Gabedit can now compute the anharmonic spectrum by QM/MMFF94 method using iGVPT2 program. Gabedit can read the harmonic and anharmonic spectra from an iGVPT2 output file.
- Energy, geometry optimization, MD, MD Conformations search by MMFF94, MMFF94s, UFF and Ghemical potentials are now supported by Gabedit via Open Babel.
- Energy, geometry optimization, MD, MD Conformations search using your own program (potential) are now supported. DFTB+ is supported via this new tool.
Instructions for compiling under Mac OSX are here https://sites.google.com/site/allouchear/Home/gabedit/download/compilation-under-macosx.
BBEdit 11.6.7 contains fixes for reported issues, as well as refinements to new features that were added in BBEdit 11.6.
Always browsing through the release notes.
When running on 10.13, the application no longer attempts to use the built-in "Consolas for BBEdit" font, because the OS won't load it and instead defaults to some proportional monstrosity. (If you are finding that this happens anyway, go to the "Editor Defaults" preferences and use the "Restore Defaults" button.)
32-bit compatibility: Since Apple has explicitly stated that macOS High Sierra will run 32-bit applications, there is no immediate compatibility concern. We do plan to release a 64-bit version of BBEdit, which we expect to have ready well before OS support becomes an issue.
An interesting post By Matthew Mayo, KDnuggets.
Here is a quick collection of such books to start your fair weather study off on the right foot. The list begins with a base of statistics, moves on to machine learning foundations, progresses to a few bigger picture titles, has a quick look at an advanced topic or 2, and ends off with something that brings it all together. A mix of classic and contemporary titles, hopefully you find something new (to you) and of interest here.
Cresset just announced the launch of Flare a new software tool to aid the understanding of protein ligand interactions.
Key new technology available in Flare 1.0:
- Visualize the electrostatics of the protein active site using protein interaction potentials
- Calculate the positions and stability of water in apo and liganded proteins using 3D-RISM
- Understand the energetics of ligand binding using the WaterSwap technique.
Flare uses the XED force field to calculate a detailed map of the electrostatic character of the protein active site. The interaction potentials provide you with vital knowledge of the fundamental processes that underlie ligand-protein binding, helping you to perfect the design of new molecules. The position and energetics of water molecules in and around the active site is of crucial importance in understanding ligand binding. Knowledge of which water molecules are tightly bound and which are energetically unfavorable can give valuable insights into structure-activity relationships and help you to decide where to place ligand atoms. Cresset’s 3D-RISM analysis utilizes the advanced inter-molecular descriptions of the XED force field to give you a water analysis you can trust.
Flare is available for Mac OSX, Linux and Windows and free evaluation is available
iChemLabs announced the release of version 8 of the ChemDoodle Web Components, the largest update of the library to date. The ChemDoodle Web Components is an industry leading HTML5 toolkit for building scientific applications for web and mobile platforms. The ChemDoodle Web Components are licensed under the open source GPLv3 license or under a commercial license.
Executive Summary: Version 8 is the largest update to the ChemDoodle Web Components library to date. The sketcher has seen significant work, with new drawing tools (rings, chains, templates, atom label tool, more). Condensed labels with abbreviations are now supported, for advanced chemistry. New 2D shapes include dynamic brackets, atom mappings and variable attachment points, while molecular surfaces (vdW, SAS, Connolly) can now be generated and rendered in 3D components. The shader system used by the 3D components has been dramatically improved for much faster performance (and new improvements added like gamma correction) and a deferred shader has been implemented to provide advanced graphics techniques like outlining, software antialiasing and screen space ambient occlusion. Shadows can now be rendered in 3D scenes. The entire website has also been improved, with new advanced tutorials for working with the sketcher to listen to user changes, or show off an advanced in browser sketcher interface that mimics the desktop software, for instance. SVG can now be exported from the ChemDoodle Web Components in addition to PNG. A new iChemLabs Cloud service allows developers to match entire mechanisms for educational eBooks and advanced reaction databases. There is a lot in this update, please see the links below for more information.
- The sketcher has been significantly developed. A new requireStartingAtom option allows you to disable to starting atom requirement while sketching. A new resizable option enables the user to resize the sketcher canvas. A new floatDrawTools option uses a floating toolbar for the drawing tools, just like the desktop software. Several new tools have been added, including an arbitrary ring size and arbitrary chain size tool. An atom label tool has been added with a text input field (like in the desktop software) to enter custom atom labels, including advanced condensed labels; space will open the text field by keyboard while the return or enter key will close it or repeat the last typed label for a hovered atom. Templates can now be added in the same manner as the desktop software using the new Templates widget; you can modify and add to the template library. The MolGrabber widget now allows the loading of any content (multiple molecules and shapes) and will insert the content in its entirety to the canvas. The MolGrabber widget will now also alert you if you press the Load button before the Show button. New buttons are available for centering the content in the sketcher as well as for horizontal and vertical flipping. The Open dialog now slides down from the toolbar as a Popover. The lasso tool and selections now use a dashed line just like in the desktop software. When using the labels tools in the sketcher, the periodic table canvas now selects oxygen by default and will revert back to label mode of the currently selected element if chosen from the toolbar. Silicon has been added to the default labels group. Placing unsaturated rings (like benzene) now better lay out double bonds to avoid overvalencing atoms. Hovering bonds are now more responsive, especially for elongated bonds. Pushers now can be set by clicking and then clicking again, no drag necessary.
- A new UIs component has been added, called Popover. A Popover is modal and can slide in from other components or appear in its own component for user input.
- Added mobile support for the UIs interface elements. For example, previously dialogs couldnt be moved on mobile devices, now they can.
- Complex labels can now be handled, with the required additional tools for parsing, formatting and rendering. With this feature, your chemical structures can contain advanced chemical labels consisting of element symbols, abbreviations (a dictionary controlled by you) and numbers and parenthesis for multiplicities. The labels are automatically formatted chemically and oriented based on least interference with surrounding bonds. Some examples include COOH, CO2Me, N3, CH2(CH2)4OH, C3H7O, Tosyl, myAbbreviation, and more. Use this to create concise publication quality figures directly in your websites.
- Added a wavy bond type.
- New shapes have been included. New 2D shapes include dynamic brackets for repeating groups, atom mappings for reactions and variable attachment points (VAPs). New 3D shapes include molecular surfaces. The ChemDoodle JSON specification has been updated to support these shapes.
- Molecular surfaces can now be generated and rendered for sets of atoms in 3D. Supported types include van der Waals, solvent accessible and solvent excluded (also known as a Connolly surface). You can control resolutions for all and the probe radius for solvent based surfaces. Rendering styles include Dots, Mesh and Solid and all colors, transparency, etc. can be controlled through visual specifications.
- The shader system for the 3D components has been redone. Several improvements in the Phong shader allow us to render higher quality graphics with lower quality meshes, leading to significant performance improvements across the entire 3D ChemDoodle Web Components.
- A deferred shader system has been developed allowing the implementation of advanced shader procedures for generating graphics. Currently implemented are outlining, screen space ambient occlusion (SSAO) and software antialiasing (FXAA). SSAO in particular is very powerful as it allows us to simulate how much ambient light is accessible to objects in crowded spaces, allowing us to shade the scene in a more accurate manner. This works on all geometries, but the feature can really be shown off in space filling all-atom models of large macromolecules.
- Shadows can now be rendered in 3D scenes. You can control the intensity of the shadows with the shadowintensity3D visual specification.
- Gamma correction has been implemented for brighter, more color accurate rendering controlled by the gammaCorrection_3D visual specification.
- The VisualSpecifications class now provides a copy() function for creating style sheet copies.
- Added a new bond visual specification for absolute saturation widths: bondsuseAbsoluteSaturationWidths2D.
- Bonds now split colors based on their substituent atom colors, with the bondssplitColor visual specification. The bondsuseJMOLColors and bonds_usePYMOLColors specifications have been removed. Use the corresponding atom specifications instead.
- Made wedge width an absolute value in line with desktop software with a default value of 6.
- Components now center 2D content much more pleasantly by calculating bounds of atom labels in addition to coordinates and using a constant internal padding.
- The preview, hover, select and error colors are now controlled by visual specifications.
- A new iChemLabs Cloud call, mechanismMatch(), is now provided to match mechanisms. You can see it in action here.
- Updated van der Waals radii data.
- Added the rest of the new elements as defined by IUPAC.
- Updated the library to use some newer standardized HTML5 functions, removing the polyfills from the ChemDoodle.extensions package.
- The PNG package has been refactored to provide both an open() function for loading the PNG into a new window and a string() method for creating a string object of the PNG content.
- A new SVG package has been added to create Scalable Vector Graphics data from the ChemDoodle Web Components, similar to the PNG package for bitmap graphics.
- Minor graphical improvements for the UIs decorations.
- Updated jQuery to version 2.2.4. Updated jQuery mousewheel to version 3.1.13.
- Updated the entire website. Added more advanced tutorials: Image Export, Initializing Components after Closing the DOM, Sketcher: Application Window, Sketcher: Listening to User Changes.
Full details of the update https://web.chemdoodle.com/installation/changelog/.
A blog post describing a package that implements an R client to extract data from the Target validation platform.
The Open Targets Platform is a comprehensive and robust data integration for access to and visualisation of potential drug targets associated with disease. It brings together multiple data types and aims to assist users to identify and prioritise targets for further investigation.
This is an alternative to the public REST API.
The Chemical Reference Resolver is an invaluable tool for quickly directing you to a publisher's webpage that contains the article you are looking for. However many of the publications are now also available on preprint servers and are accessible for free even if the final publication is behind a paywall.
To search for open access versions simply prepend your doi string with the word "oadoi" and press Enter.
Full details are in this blog post http://kovsky.net/blog/posts/oadoi-resolving.
StarDrop 6.4 now links prepared 3D docking and alignment models with data visualisation, 2D SAR analyses and predictive models in a single interface.
Computational chemists can make their validated 3D models available to their colleagues via StarDrop’s Pose Generation Interface, which is compatible with software from major computational chemistry providers, including:
- FlexX™ – BioSolveIT
- Gold™ – Cambridge Crystallographic Data Centre
- MOE™ – Chemical Computing Group
- AutoDock Vina – The Scripps Research Institute
- POSIT™ – OpenEye Scientific
- …extendable to other third party applications.
The Pose Generation Interface communicates with a Pose Generation Server, on which computational chemists can easily publish their validated docking or 3D alignment models. These are made instantly available for StarDrop users to submit their compounds and the resulting poses, protein structures and scores are returned directly to StarDrop for visualisation and analysis.
The Pose Generation Server can be installed wherever you run your 3D modelling software, supporting Linux, Windows® and Mac®
There are more details in the poster presented at the Spring ACS 2017.
UKeiG presents the Tony Kent Strix Award in partnership with the International Society for Knowledge Organisation (ISKO UK) and the British Computer Society Information Retrieval Specialist Group (BCS IRSG). The award is sponsored by the Royal Society of Chemistry Chemical Information & Computer Applications Group.
The UK electronic information Group (UKeiG) is now seeking 2017 nominations for this prestigious award.
The Tony Kent Strix Award is given in recognition of an outstanding practical innovation or achievement in the field of information retrieval in its widest sense, including search and data mining, for example. This could take the form of an application or service, or an overall appreciation of past achievements from which significant advances have emanated. The award is open to individuals or groups from anywhere in the world.
The deadline for nominations is Thursday 31st August 2017.
Nominations should be for achievement that meets one or more of the following criteria:
- A major and/or sustained contribution to the theoretical or experimental understanding of the information retrieval process
- Development of, or significant improvement in, mechanisms, a product or service for the retrieval of information, either generally or in a specialised field
- Development of, or significant improvement in, easy access to an information service
- Development and/or exploitation of new technologies to enhance information retrieval
- A sustained contribution over a period of years to the field of information retrieval for example, by running an information service or by contributing at national or international level to organisations active in the field.
Key characteristics that the judges will look for in nominations are innovation, initiative, originality and practicality.
The information to be supplied in the nomination should comprise:
- The name, institutional address and qualifications of the nominee
- A brief biography (not more than one page of A4)
- A relevant bibliography (i.e. not comprehensive but including the key publications relevant to the nomination)
- A justification for the nomination, of not more than one page of A4, showing clearly which of the Strix award criteria the nominee meets and how the criteria are met
- Additional material (e.g. letters of support - letters from past winners would be especially valuable).
It is possible that the Award Committee will request additional information from the nominators for those nominees considered suitable candidates for the award.
Nominations for the 2017 award should reach the judges by Thursday August 31st 2017 and be emailed to:
John Wickenden – Hon. Secretary UKeiG email@example.com
cc-ed to Gary Horrocks - UKeiG administrator firstname.lastname@example.org
cc-ed to Sue Silcocks – Hon. Treasurer UKeiG email@example.com
Just added Learning Stereochemistry VR to the mobile science website.
Learning StereoChem VR is a mobile app where you can experience stereoisomers in a virtual reality, using Google Cardboards. Stereoisomers have the same molecular formula and the same connectivity of atoms but a different arrangement of atoms in space. Stereoisomers are non-superimposable on their mirror image. Proteins can often distinguish between these mirror images. In this app we explain the importance of stereochemistry.
This app comes from the same group who created Learning MacroMols VR and Learning Carbons VR. Learning MacroMols VR is a mobile app where you can experience macromolecules such as DNA, RNA, carbohydrates and protein structures (from the PDB – Protein Data Bank) in a virtual reality, using Google Cardboards. Learning Carbons VR is an educational virtual reality (VR) app where students can learn about the various forms of carbon.
The use of VR in teaching looks to be a growing trend.
I recently wrote a review of Reaction Workflows, a web-based tool that allow users to build workflows from nodes that provide inputs and outputs or perform actions, including ones to perform reaction-, scaffold-, and transform-based enumeration, and it is all done within a web browser interface using drag and drop. Whilst you can draw input structures one of the real strengths is the ability to import pre-categorised reagent files e.g.Acid Chlorides or secondary amines. This script is intended to help with this within Vortex.
This script is a variation of the high performance sub-structure search scripts described previously, however instead of simply flagging the presence (or absence) of a SMARTS query we provide a count of the number of times a SMARTS query is identified within a molecule. The script uses all available cores and is thus capable of running multiple queries in parallel and can thus handle very large datasets. The script currently contains around 70 different SMARTS queries for both functional groups and atom counts and I'd be happy to add any suggestions.
The all new SeeSAR 6 provides you with a completely redesigned and now fully customizable GUI. You can choose between different bright and dark themes and GUI layouts so that you can optimally adapt SeeSAR for different use cases.
The new design is more streamlined and customizable. Instead of having 8 different kinds of buttons in different regions of the application, we now have just a main menu top left and a toolbar top right. The main menu changes depending on the mode of use (editing, site definition, ...), while the toolbar stays the same throughout. This way you are never overwhelmed with choices, but are only presented with options that you may need. Depending on you current use case, you may also want to change the overall layout (many molecules ⇒ tables to the left; many properties ⇒ tables below to make use of the whole width; 2 monitors ⇒ tables docked out) and/or the overall appearance (bright theme for presentations; dark theme for desktop work; we have also integrated a color blindness mode just in case).
In order to give you a jump start when you begin working with SeeSAR (both as a newcomer, as well as a seasoned user of the old GUI design), we have introduced an in-application help facility in this new version. First of all, upon starting the tool for the first time or after a long break in use, SeeSAR offers you a short introductory slide show, reminding you of a few basics that can make life a lot easier. But you can also now request help from within the application with a click on the lifesaver button. The help window then shows you – context dependent – explanations on the mode in which you are currently working or on the functions that you are trying to use so you can leave the help window open, consulting it when you need it. Of course you may also navigate between help pages in the help window and from there access online resources such as tutorial videos.
There is also a free webinar: introduction to SeeSAR 6.0
Greg Landrum posted the following to the RDKit users and since a couple of the Jupyter Notebooks I've published make extensive use of RDKit I thought I'd flag it.
As many of you are no doubt aware, the Python community plans to discontinue support for Python 2 in 2020. A growing number of projects in the Scientific Python stack are making the same transition and have made that explicit here: http://www.python3statement.org/
I will be adding the RDKit to this list. The RDKit will switch to support only Python 3 by 2020. At some point between now and then - likely during the 2018.09 release cycle - we will create a maintenance branch for Python 2 that will continue to get bug fixes but will no longer have new Python features added. This branch will be maintained, and we will keep doing Python 2 builds, until 2020 when official Python 2 support ends.
Additionally, starting during the 2018.03 release cycle we will accept contributions for new features that are not compatible with Python 2 as long as those features are implemented in such a way that they don't break existing Python 2 code (more on this later). This will allow members of the RDKit community who have made the switch to Python 3 to start making use of the new features of the language in their RDKit contributions.
If you have not made the switch yet to Python 3: please read the web page I link to above and take a look at the list of projects that have committed to transition. The switch from Python 2 to Python 3 isn't always easy, but it's not getting any easier with time and you have a few years to complete it. There are a lot of online resources available to help.
Best Regards, -greg
The list of projects that will be making the transition so far includes; IPython, Jupyter notebook, pandas, Matplotlib SymPy, Astropy, Software Carpentry, SunPy xonsh, scikit-bio, PyStan, Axelrod osBrain, PyMeasure, rpy2, PyMC3, FEniCS, An Introduction to Applied Bioinformatics, music21, QIIME, Altair, gala, cual-id, CIS
ROCS is a shape-based superposition method. Molecules are aligned by a solid-body optimization process that maximizes the overlap volume between them. Volume overlap in this context is not the hard-sphere overlap volume, but rather a Gaussian-based overlap parameterized to reproduce hard-sphere volumes. ROCS uses only the heavy atoms of a ligand, hydrogens are ignored.
ROCS is built on top of the OpenEye Toolkits v2017.Feb libraries to ensure that ROCS and the ancillary programs are taking advantage of state-of-the-art improvements in the underlying programming libraries. This version of ROCS fixes a bug that prevented molecule streaming using pipes and named pipes on Linux and OS X systems. ROCS now accepts molecule streams or named pipes as database files.
Support for Mac OS X 10.10, 10.11, and MacOS X Sierra 10.12 has been added. Mac OS X 10.8 and 10.9 are no longer supported.
Clustering is an invaluable cheminformatics technique for subdividing a typically large compound collection into small groups of similar compounds. One of the advantages is that once clustered you can store the cluster identifiers and then refer to them later this is particularly valuable when dealing with very large datasets. This often used in the analysis of high-throughput screening results, or the analysis of virtual screening or docking studies.
On this page I've explored multiple options for clustering, from Open Source toolkits to sophisticated desktop applications.
ToMoCoMD-CARDD is an interactive and user-friendly free multi-platform framework designed to calculate 2/3-D numerical descriptors (indices) for molecular structures, with the objective of characterizing or discriminating among them. It can be downloaded here http://tomocomd.com/software.
Elemental has been updated to version 2.1 adding support for iOS 11 (64-bit support)
Elemental is the free Dotmatics chemistry sketch app.
There are more mobile science apps here
Researchkit has been updated to version 1.5
ResearchKit is an open source framework introduced by Apple that allows researchers and developers to create powerful apps for medical research. Easily create visual consent flows, real-time dynamic active tasks, and surveys using a variety of customizable modules that you can build upon and share with the community.
You can download it from GitHub.
Pred-skin is a new mobile app for predicting skin toxicity. Pred-skin is a web app that accesses a web service http://www.labmol.com.br/predskin/ for the calculation and thus requires internet access. The web service also allows bulk predictions.
Chemically-induced skin sensitization is a complex immunological disease with a high impact on the quality of life and working ability. Despite some progress in developing alternative methods for assessing skin sensitization potential of chemical substances, there is no single in vitro test that correlates well with human data. Machine Learning (ML) models provide a rapid screening approach and contribute valuable information for the assessment of chemical toxicity. The Pred-Skin App is an alternative method for assessing skin sensitization potential of chemical substances.
Full details are in the publication Pred-Skin: A Fast and Reliable Web Application to Assess Skin Sensitization Effect of Chemicals DOI There are many more mobile apps available for science on the mobile science website.
As highlighted recently SketchEl2 a chemical drawing package is now open source.
The SketchEl 2 project is underway as a desktop app, based on web technology and delivered as an Electron package. The GitHub repository is now public, on account of there being enough functionality to be arguably useful. This is a very early release, so do be ready to give some useful feedback if you feel so inclined to try it out.
The repository can be found here https://github.com/aclarkxyz/web_sketchel2
The Data Analysis Tools page contains a list of applications for data analysis that run under Mac OSX, in addition I've also included some other useful tools. Included in the list is Data Extractor.
Data Extractor allows to extract data in a sparse format contained inside various files and collect the data you need in an internal structured table. Collected data can be exported at any time in various format (CSV, TSV, HTML, Custom). Data extractor can parse thousands and thousands of file in few seconds and collect the data inside. It uses simple smart instructions about how to recognize the data you need, how to extract them and where to put these data inside a structured table, ready to be exported.
Version 1.5 updates:
- Additional force option: 'Prefix at Start of Line'
- Extraction algorithm improved
- Bug fix extracting data with start tag having a space as first character
- Other minor bug fix
- Optimized for macOS 10.12 Sierra
A while back I published two scripts that use UniChem a web resource provided by the EBI, a 'Unified Chemical Identifier' system, designed to assist in the rapid cross-referencing of chemical structures, and their identifiers, between multiple databases.
Chambers, J., Davies, M., Gaulton, A., Hersey, A., Velankar, S., Petryszak, R., Hastings, J., Bellis, L., McGlinchey, S. and Overington, J.P. UniChem: A Unified Chemical Structure Cross-Referencing and Identifier Tracking System. Journal of Cheminformatics 2013, 5:3 (January 2013). DOI: http://dx.doi.org/10.1186/1758-2946-5-3
The first script uses the ChEMBL ID to search for other identifiers, the second script allows more flexible searching using any of the identifiers available within UnicChem. One of the identifiers returned is from the PDBe (Protein Data Bank Europe) and represents the ID of the ligand in the PDB. Whilst this is interesting it would also be very useful to have the identity of the crystal structures that contain the ligand. Fortunately PBDe provide a series of web services that can be used to interrogate the database, together with a really useful page to help build the calls.
Crystal14 Version 1.0.4 is mainly a bugfix release. All users are encouraged to upgrade to v1.0.4 as soon as possible.
This is the list of options which have been fixed in the v1.0.4 version of CRYSTAL14:
- Electronic band structure for open-shell systems (asymmetric k-points only)
- Piezoelectricity of 1D and 2D cases (non-periodic directions fixed)
- Piezoelectricity for open-shell systems
- BREAKELAST option restored
- ATOMINSE+SUPERCELL combination fixed
- Cell gradients for charged systems
- Range-separated hybrids (conflict with bipolar approximation fixed)
- Some static limits for CLUSTER option have been relaxed
- Small fixes (normalization, k-points coordinates) in phonon bands and density-of-states
- CUBE format for 3D plots of charge density and electrostatic potential fixed
- Various fixes in restart options of vibration frequencies + IR and Raman intensities calculation
- HJS exchange hole for open shell systems. This affects HSE06, HSEsol, HISS, LC-wPBE, LC-wPBEsol and LC-wBLYP functionals.
- Fixes in the POTC option
The Royal Society of Chemistry Chemical Information and Computer Applications Group (CICAG) are conducting a survey to find out more about the way that scientists use the various social media channels.
The survey is very short and feedback would be appreciated from everyone, you don't have to be a member of the RSC (or CICAG) to contribute.
The survey can be found here https://www.surveymonkey.co.uk/r/YSYFRDP.
The Chemical Information and Computer Applications Group (CICAG) is one of the RSC’s many member-led Interest Groups.
A recent paper describes Psi4 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and Interoperability DOI
Psi4 is an ab initio electronic structure program providing methods such as Hartree–Fock, density functional theory, configuration interaction, and coupled-cluster theory. The 1.1 release represents a major update meant to automate complex tasks, such as geometry optimization using complete-basis-set extrapolation or focal-point methods. Conversion of the top-level code to a Python module means that Psi4 can now be used in complex workflows alongside other Python tools.
Psi4 1.1 can be downloaded from here with versions supporting Python 2.7, 3.5 and 3.6.
Note the installation instructions for Mac: Install XCode via the App Store, Make sure you open XCode and accept the license agreement after you install.
Apple Education has just announced a new app development curriculum designed to teach students how to start using Swift to create fully functional iPhone apps.
The course is available for free on iBooks and can be read on iPad, iPhone, and Mac..
This course is designed to teach you the skills needed to be an app developer capable of bringing your own ideas to life. Whether you’re new to coding or want to expand your skills, by the end of this course you should be able to build a fully functioning app of your own design.
The 900 page book is available here https://itunes.apple.com/gb/book/app-development-with-swift/id1219117996?
I just came across a publication DOI describing ARIA2 (Ambiguous Restraints for Iterative Assignment) is a software for automated NOE assignment and NMR structure calculation.
ARIA comes as a software library written in the object-oriented programming language Python. The modular design makes it easy for the user to extend and modify the program. The GUI is based on the graphics libraries Tcl/Tk and Tix, interfaced by Python.
ARIA runs on Linux, SGI machines and Mac OS X.
More details can be found on the website http://aria.pasteur.fr.
I've added ARIA2 to the spectroscopy page.
The generation of multiple conformations is an important step in a number of operations from input to ab initio calculations to providing input files for docking studies. A recent paper compared seven freely available conformer ensemble generators: Balloon (two different algorithms), the RDKit standard conformer ensemble generator, the Experimental-Torsion basic Knowledge Distance Geometry (ETKDG) algorithm, Confab, Frog2 and Multiconf-DOCK DOI, and also provided a dataset of ligand conformations taken from the PDB.
A recent twitter discussion involving Greg Landrum and David Koes prompted Greg to publish a blog post describing conformation generation within RDKit. The post compares using distance geometry to select diverse conformations versus an approach that combines the distance geometry approach with experimental torsion-angle preferences obtained from small-molecule crystallographic data (ETKDG). He also looks at the impact of force-field minimisation.
A really interesting read with code provided.
Some time ago I published an AppleScript that allowed users to make use of the excellent Organic Chemistry Reference Resolver.
The Chemistry Reference Resolver serves to quickly direct you to a publisher's webpage that contains the article you are looking for: You type-in the reference The Resolver determines whether it is a journal citation, a DOI, a Sigma-Aldrich chemical search, or something more esoteric Based on the input, it then redirects you to the publisher's webpage – straight to the paper (or its nearest approximation) Many formats are supported including vaguely defined "lazy citations", such as "perkin1 2002 2733".
I was really delighted to hear recently that Brian Myers had customised the script to fit in better with his workflow. Simply copy the reference text to the clipboard and when you activate the script you can search for the reference immediately. Both versions of the script are available here.
I see that OpenCL 2.2 has been released and reading through the press release there are a couple of notes that might be of wider interest.
By finalizing OpenCL 2.2, Khronos has delivered on its promise to make C++ a first-class kernel language in the OpenCL standard,” said Neil Trevett, OpenCL chair and Khronos president. “The OpenCL working group is now free to continue its work with SYCL, to converge the power of single source parallel C++ programming with standard ISO C++, and to explore new markets and opportunities for OpenCL — such as embedded vision and inferencing. We are also working to converge with, and leverage, the Khronos Vulkan API — merging advanced graphics and compute into a single API.
Vulkan is a new generation graphics and compute API that provides high-efficiency, cross-platform access to modern GPUs used in a wide variety of devices from computers and consoles to mobile phones and embedded platforms.
There is page of GPU accelerated applications in science applications here
Cardiogram allows you to join an ambitious study to detect the most common heart arrhythmia using your smart watch. Contribute your data and save lives.
Each year, more than 100,000 strokes are caused by an abnormal heart rhythm called atrial fibrillation. In atrial fibrillation, electrical conduction in the heart becomes disorganized. The upper chambers may beat 300-600 times per minute. The lower chambers may beat at a normal rate, but irregularly. Atrial fibrillation is treatable, but many people don't feel symptoms, so it often goes undiagnosed.
There are more mobile science apps here
Anyone who has touched upon scripting/automation on the Mac will no doubt have heard of Sal Soghoian so when I got this message recently I thought I'd better pass it on.
Sal here, with something pretty cool to share with you. We’ve started a new conference to bring together the Apple automation and scripting community!
The conference is called CMD-D (pronounced “Command-D”), and it will be held August 9th at the Santa Clara Convention Center. It’ll be a full day of exploring the current state of automation technology on both Apple platforms, sharing ideas and concepts, and showing what’s possible—all with the goal of inspiring and furthering development of your own automation projects. To assist in this exploration of all things Automation, I’ve invited some of my smartest friends to present sessions focused on their own areas of automation expertise, on macOS and iOS. And, for those new to automation, we’re also planning a Scripting Boot Camp on August 8th. I’m really excited about CMD-D. Finally, the Apple automation community has its own conference. If you use automation, create automation or develop software, this is your conference too.
Registration for CMD-D is open now! http://www.cmddconf.com.
Workflow tools have become increasingly popular Pipeline Pilot, Knime and Taverna and perhaps the best known. Most are desktop client based but some have a web page that allow users to run protocols that expert users have created.
Dotmatics Reaction Workflows (RW) is a web-based tool that allow users to build workflows from nodes that provide inputs and outputs or perform actions, including ones to perform reaction-, scaffold-, and transform-based enumeration, and it is all done within a web browser interface using drag and drop. I've been looking at reaction workflow for enumerating a potential library array.
I regular get several hundred spam emails every day, I use an aggressive SPAM filter but I still have to spend time browsing through the spam folder everyday to ensure nothing important has been caught. This weekend however I've only had a handful of spam emails, Wondering if all those people generating the spam were using Windows XP and got hit by the recent cyber attack?
Sci-Hub is a web service that provides free access to research articles and latest research information, the website uses donated library credentials of contributors to circumvent publishers’ paywalls and thus downloads large parts of their collections. In 2016 Sci-Hub released data on ~28 million downloads done through the service and in 2017 Sci-Hub released the list of ~ 62 million Digital Object Identifiers (DOIs) of the content they have stored.
A recent publication DOI describes a detailed analysis of Sci-Hub usage and as you can see in the plot below taken from the article chemistry journals (shown in red) are particularly popular.
Scaffold Hunter is a chemical data organization and analysis tool and that has been continuously enhanced since the start of its development in 2007. The platform-independent open-source tool was first released in 2009 and provided an interactive visualisation of the so-called scaffold tree, which is a hierarchical classification scheme for molecules based on their common scaffolds. A recent publication describes recent extensions that significantly increase the applicability for a variety of tasks DOI.
When I first opened the application I did not find it particularly intuitive, fortunately there is a online tutorial and sample datasets available.
aRMSD is an open toolbox for structural comparison between two molecules with various capabilities to explore different aspects of structural similarity and diversity. Crystallographic data provided from cif files is fully supported and the results can be rendered with the help of the vtk package.
A. Wagner, H.-J. Himmel, J. Chem. Inf. Model, 2017, 57, 428-438 DOI
Chemical Structure Representation: What Would Dalton Do Now? should be an interesting meeting looking at the different way we represent structures. Thursday 22 June 2017 Department of Chemistry, University of Liverpool, Liverpool L69 7ZD.
A few of the lecture titles that caught my eye:
- Biology: bigger models, bigger confusion
- Extracting Medicinal Chemistry Knowledge by a secure Matched Molecular Pair Analysis Platform: standardization of SMIRKS enables knowledge exchange
- Indescribable structure: finding words for the future
- InChIs are part of the solution
- Chemical structure representation challenges encountered when curating the CSD
- Chemical Structure Representation of Inorganic Salts and Mixtures of Gases: A Newer System of Chemical Philosophy
Apparently Tours of the new Central Teaching Hub at the University of Liverpool will also be available. Poster deadline 22 May.
There is also another meeting coming up later this month which could be of wide interest.
Just looking at the release notes for ADF2017 and support pages and a couple of things caught my eye.
The python distribution shipped with ADF was upgraded to python 3.5. Among others, new and updated modules include the iPython interpreter for easier development of python codes, a number of useful packages such as numpy 1.11.3 / scipy 0.18.1, ASE 3.13.0, matplotlib and RDKit 2016.09.
The Mac OSX version no longer requires XQuartz and is much faster in visualizing large systems.
It has been a little while but ChemDoodle 3D is out, and looking at the new features it was certainly worth the wait, this is a major upgrade!
New features in ChemDoodle 3D v3:
- Faster and more advanced shaders for the most realistic graphics or captivating cartoon rendering. There are now 6 shaders to choose from.
- Fully customizable and dynamic real-time shadow rendering.
- Molecules can now be built using intuitive tools and a continuous running optimization (using the new Minimizer widget) to allow you to build accurate models and the specific conformations you desire. It is a lot of fun to physically interact with the structures you build!
- New bond types, more aromatic ring representations, more cheminformatics functions.
- Distances can now be measured between any combination of bond centers and atoms; previously only atoms were allowed. Visual specifications for all shapes can now be independently edited.
- Fully customizable surfaces can now be built for selections of atoms.
- Selector tools have been added, and you can now select objects by lasso and rectangular marquee.
- Our interface engine is now fully implemented including drawing toolbars, widgets, autosaving, workspace control and more.
- Style sheets (and scene settings files) can now be created, saved and loaded.
- Quaternions can now be used for all rotations, instead of just X-Y axis rotation.
- Full support for the new RCSB MacroZZmolecular Transmission Format.
- A more advanced copy and paste system.
- After effects are new multipass shader options that provide additional graphical effects. Blurring and outlining are currently available.
- Outlines are now rendered for highlighted and selected objects.
- Model settings in the Visuals panel in Preferences are now organized by model type.
- A new Custom Element Color Set. Color choosers have been upgraded and now affect graphics in real time. Improved MacOS look and feel.
- Added the last of the new element names recommended by IUPAC. Added more published van der Waals values.
- Polishing, new icons, and performance improvements affecting just about every asproect of the product, from picking to animations to rendering and saving images.
This is a new release of DOCK with updated scoring functions including the new pharmacophore matching similarity score and a completely revamped Descriptor Score that allows for different combinations of various scoring functions to be used simultaneously From the readme
NEW IN DOCK 6.8
New Scoring Functions Two new scoring functions were added: pharmacophore score , and descriptor score [see the manual].
Pharmacophore: Calculates the pharmacophore overlap between a candidate and a reference molecule. In addition, the python wrapper, mol2bild.py, can be employed to visualize the pharmacophores.
Descriptor Score: Descriptor Score was completely overhauled. Presently, descriptor score is now a wrapper that allows multiple scoring functions to be employed simultaneously. Please refer to the manual for the complete list of scoring functions supported by descriptor score.
Four similarity-based scoring functions were added as part of descriptor score: pharmacophore score, Tanimoto score, Hungarian matching similarity score, and volume overlap score. Hungarian matching similarity score, Tanimoto score and volume overlap score, new to DOCK, can only be called using descriptor score.
Internal Energy Scoring Function Optimization of the internal energy scoring function code and the addition of two parameters:
a) The code has been optimized for calculating the repulsive VDW term. "internalenergyrep_exp", when set to its default value of 12, results in a significant speedup in certain cases. Values other than 12 are computed as in previous versions of DOCK.
b) The term "internalenergycutoff" has been added such that all conformers with an internal energy greater than the cutoff are pruned.
c) The addition of the term "pruningconformerscorescalingfactor", a divisor of the pruningconformerscore_cutoff, ensures that pruning becomes more stringent as flexibly-grown molecules proceed layer-by-layer.
Miscellaneous DOCK now supports builds using Intel compilers with either MPICH2 or Intel MPI parallelism.
I just got this message
We are proud to announce the 2017 release of the ADF Modeling Suite, with excellent contributions from our collaborators and the continued efforts of the SCM team in Amsterdam.
Exciting new features include
- Many new NLO properties (TPA, THG, ...): Hu, Autschbach & Jensen
- Constrained DFT with excited states: Ramos & Pavanello
- LFDFT for d-d and d-f transitions: Ramanantoanina & Daul
- CV-DFT for singlet-triplet excitations: Krykunov, Senn, Park & Seidu
- Faster periodic response with TD(C)DFT, including 2D systems: Raupach
- VCD analysis tools: Nicu
Reactivity & Analysis-
- Latest xc functionals (SCAN, MN15-L, ....): interface to libxc 3.0
- Special points, fat bands and improved pDOS analysis
- GUI support for NEGF with BAND (Thijssen group, includes self-consistent NEGF, gate & bias potential, spin transport) and post-SCF DFTB-NEGF (Heine group)
- FDE + local COSMO: Goez & Neugebauer
- Reactivity descriptors from conceptual DFT and QTAIM: Tognetti & Joubert
- Geometry optimization with SpinFlip in QUILD: Swart
- Spin-polarization and l-dependency for DFTB: Melix, Oliveira, Rueger, Heine
- Much faster periodic DFTB(+D) optimizations, latest DFTB.org parameters freely available
- eReaxFF including explicit electrons: based on Islam, Verstraelen & van Duin
- Controllable mass-scaling for force bias Monte Carlo ReaxFF: Bal & Neyts
- Improved VLE, LLE, IDAC, kOW with reparameterized COSMO-SAC: Chen & Lin
GUI & Builders-
- Quantum ESPRESSO: GUI interface & binaries
- MOF builder and UFF4MOFsII: Coupry, Addicoat, Heine
- Much faster visualization of large and periodic systems
- Set up and visualize 'molecule gun' calculations with ReaxFF
For a more comprehensive list and details see: www.scm.com/support/release-notes
A great tutorial describing how to use 'Biopandas' MOL2 DataFrames to analyze molecules conveniently.
The Tripos MOL2 format is a common format for working with small molecules.
The Royal Society of Chemistry Twitter Poster Conference is an online event held entirely over Twitter to bring members of the scientific research community together to share their research, network and engage in scientific debate. Building upon the success of the previous two Analytical Science Twitter Poster Conferences, the 2017 poster conference encompassed all areas of the chemical sciences. The conference reached the scientific research community around the world, achieving 1,650 contributors, 6,473 tweets, an audience of 2,770,749 and 11,841,519 total impressions.
This new version of SeeSAR an interactive tool for designing/improving ligands for drug discovery. This update comprises another milestone in the evolution of this lightweight 3D modeling package, namely its ability to manage multiple protein structures simultaneously. Oftentimes, you may need to take account of multiple, related protein structures, perhaps either to identify the differences while aiming to achieve specificity, or – just the opposite – to find commonalities, such as when you are trying to ensure all variants of a protein will likely be inhibited. In this first implementation of the multi-protein feature, it is not yet possible to align protein structures but it is necessary to work with pre-aligned structures. Loading multiple proteins
Loading a protein does not now start a new project, but instead the new protein is simply added to a table of loaded proteins. In order to visualize the binding of ligands from the protein file, first select the protein of interest and then select one of the ligands listed in the table. As before, any of these bound ligands can be copied to the molecules table with a click on the molecule icon in the ligand table row. Handling multiple proteins
By default, the proteins chains are colored according to the same coloring scheme as before, with each chain in a different color. In the protein table you may set a unique color for a protein to ease identification that will be used for all components of that protein. If you edit a protein, the edited version of the protein will simply be appended to the table without overwriting the original. It is of course also possible to delete proteins from the table. Finally, you may choose the protein to be used for defining a common binding site from the table, just click the icon to start the binding site definition. Once a common binding site has been defined, a little binding site icon indicates which protein was used. Note that only this particular protein is used for the generation of poses, as well as for optimization and affinity estimation, i.e. the Hyde atom coloring on molecules is shown with respect to this protein.
Viewing multiple proteins
Once a common binding site has been defined on one protein, the binding site itself is shown in greater detail. Now however, the regions of the other proteins in the vicinity of the common binding site are also shown in greater detail. This allows you to see the detail you need when seeking out differences or commonalities but the view may, however, become a little crowded. An enhanced menu under the protein visualization icon allows you to switch on and off different protein components (secondary structure, binding site amino acids, ligands, waters and metals) individually or as a group, and you may also change the visibility of entire proteins at once, all making handling of the view very flexible depending on your needs.
We have fixed some seldom occurring but still irritating issues with the 3D editor and also implemented the possibility to restrict the number of CPUs that SeeSAR may recruit for its computation on the command line. The option --thread-count allows you to limit the number of parallel compute threads as best suited. This feature is particularly useful if you run SeeSAR on a cluster which is controlled by a batch queuing system.
There is a review of an earlier version of SeeSAR here.
Mnova 11.0.4 (April 2017) has been released, this is another minor release with some bug fixes such as:
- Improved NUS processing algorithm: some 2D experiments that showed unexpected noise artefacts are now processed properly by the improved NUS processing algorithm.
- HSQC stripped transformed in Topspin files loads spectra correctly referenced.
- All shortcuts (Mac version) are now fully functional.
- Agilent LCMS files with negative ion traces are now detected appropriately.
Mnova is a multipage, multivendor, multitechnique and multiplatform analytical chemistry software suite designed as a container for various plugins.
As of Safari Technology Preview Release 26, and WebKit Nightly Build, a WebGPU prototype is available for you to experiment with on macOS.
To enable WebGPU, first make sure the Develop menu is visible using Safari → Preferences → Advanced → Show Develop menu in menu bar. Then, in the Develop menu, make sure Experimental Features → WebGPU is checked. More details and demos here
The latest version of Pages (version 6.1) and iBooks Author (version 2.0) include support for LaTeX and MathML, this is an interesting addition that will be of interest for many scientists
LaTeX is a high-quality typesetting system; it includes features designed for the production of technical and scientific documentation. LaTeX is the de facto standard for the communication and publication of scientific documents.
I've had a quick look at it here.
There is a listing of software reviews here.
Back in March 2015, Apple Inc announced ResearchKit, a novel open-source framework intended to help medical researchers to easily create apps for medical studies. Since then there have been a number of mobile apps created to make use of this framework and a few have now made it into the literature, “Back on Track”: A Mobile App Observational Study Using Apple’s ResearchKit Framework DOI was designed to help understand decision making in patients with acute anterior cruciate ligament (ACL) ruptures. The Asthma Mobile Health Study, a large-scale clinical observational study using ResearchKit DOI enabled prospective collection of longitudinal, multidimensional data (e.g., surveys, devices, geolocation, and air quality) in a subset of users over the 6-month study period. The Mole Mapper Study, mobile phone skin imaging and melanoma risk data collected using ResearchKit DOI Skin cancer research is particularly amenable to this approach, as phone cameras enable self-examination and documentation of mole abnormalities that may signal a progression towards melanoma.
At the end of last year the RSC CICAG ran a one day meeting looking a mobile apps in chemistry. With the Spring meeting of the ACS in San Francisco starting today I'd be interested in hearing about any new Mobile apps for chemistry. You can download the app for the meeting here.
The ACS Mobile Meeting Application is your full-featured guide to manage your experience at the 253rd ACS National Meeting & Exposition in San Francisco, CA (April 2-6, 2017).
You can browse mobile science apps for iOS here.
A reader recently wrote in asking about the availability of an elemental analysis app for Mac. I know there used to be a dashboard widget but that seems to have disappeared, and of course a number of chemical drawing packages and websites offer microanalysis and molecular weight calculations. However I don't think there is a simple app for calculations of % elemental composition by weight for comparison with microanalytical results?
If there is please let me know.
AFITT is a crystallographic tool for correctly placing small molecules in real-space density. AFITT merges OpenEye’s Shape and MMFF technologies into a new combined forcefield that fits small molecules into crystallographic density while maintaining excellent chemistry.
Support has been added for Ubuntu 16, OSX 10.10, OSX 10.11, and OSX 10.12. OSX 10.7, OSX 10.8, OSX 10.9, SuSe 11, and Redhat 5 x86 are no longer supported
This release adds support for Coot 0.8. Coot 0.6 and earlier versions are no longer supported.
FLYNN (the ligand fitting application) comes bundled with a refinement dictionary writer, WRITEDICT, that uses the MMFF94 force field to derive geometrical constraints for input ligands or protein-ligand complexes. The output dictionaries enforce, as closely as possible, the input ligand’s geometries while allowing the refinement programs to modify the geometry as needed. This version corrects a serious error in which WRITEDICT wrote incorrect bonds lengths for 5-5, 5-6 heterocycle ring systems. A bug that caused PDB remark data that was more than 72 characters long to be clipped from the refined output has been fixed. This only occured when the input and output file formats were both PDB.
Mac OS X 10.12.4 improves the stability, compatibility, and security of your Mac, and is recommended for all users. This update:
- Adds Night Shift for automatically shifting the colors in your display to the warmer end of the spectrum after dark.
- Adds Siri support for cricket scores 😄, schedules, and player rosters from the Indian Premier League and International Cricket Council.
- Adds Dictation support for Shanghainese.
- Improves right-to-left language support for the Touch Bar, toolbar, and visual tab picker in Safari.
- Resolves several PDF rendering and annotation issues in Preview.
- Improves the visibility of the subject line when using Conversation View in Mail.
- Fixes an issue that may prevent content from appearing in Mail messages.
- Adds support for more digital camera RAW formats.
Xcode 8.3 brings faster builds for large projects containing both Objective C and Swift. Siri support in iOS simulator. Xcode 8.3 no longer supports Swift 2.3 so you will need to update.
Also updates for Pages, Keynote and Numbers.
Perkin-Elmer have just announced the ChemDraw Innovation Challenge - a forum designed to shape the future of Chemdraw
For the past 30 years, ChemDraw has been known around globe as the premier chemical drawing tool for chemists and biologists alike. While each version has brought more powerful features (many of which came from feedback from our passionate user base), we’ve all had that moment where we wanted ChemDraw to do [X]. We want to hear your ideas, suggestions for new features, new third-party applications we should integrate and more. The sky's the limit - big or small, all ideas are welcome!
I'm running out of storage space on my Synology NAS and I"m thinking of adding another device.
Current options are an updated 2 bay device Synology DS213J 10TB (2 x 5TB) 2 Bay Desktop Network Attached Storage which can accommodate upto 10TB of storage. Alternatively I could go for the 4-bay device Synology DS416 12TB (4 x 3TB WD RED) 4 Bay Desktop NAS which offers greater capacity, or similar capacity with 4 smaller drives.
Any views on the reliability of the larger capacity HDDs ?
The 3D printing page always attracts a regular stream of readers so I thought I'd flag this article from HP.
Digital manufacturing with 3D printing has the potential to disrupt the $12 trillion global manufacturing sector, said Timothy Weber, HP vice president and general manager of 3D materials and advanced applications.
HP began shipping its model 4200 Multi Jet Fusion units with Voxel-level 3D printing, that has a 21-micron resolution.
This is a recording of the March 2017 Global Health Compound Design meeting. A webinar demonstrating using Jupyter, the free iPython notebook.
How to get started
Accessing Open Source Malaria data
Calculating physicochemical properties and plotting
Predicting AMES activity.
The latest update to ORCA has just been released.
The program 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. Due to the user-friendly style, ORCA is considered to be a helpful tool not only for computational chemists, but also for chemists, physicists and biologists that are interested in developing the full information content of their experimental data with help of calculations.
New Features of Version 4.0:
- Linear scaling DLPNO-CCSD(T) open shell. New restricted open-shell formulation
- Linear scaling DLPNO-MP2 (RHF and UHF)
- Linear scaling DLPNO-MP2-F12 (RHF)
- Linear scaling DLPNO-CCSD(T) (the 2013 implementation is still available)
- Linear scaling DLPNO-CCSD(T) local energy decomposition scheme
- Linear scaling DLPNO-CCSD closed shell density
- Linear scaling cluster in molecule (CIM): MP2, CCSD(T), DLPNO-CCSD(T)
- Linear scaling DLPNO-NEVPT2
- Updated interface to BLOCK 1.0
- Closed shell EOM-CCSD energies
- Closed shell STEOM-CCSD energies
- Partial PNO-EOM-CCSD method for excited states
- Partial PNO-STEOM-CCSD method for excited states
- DLPNO-CCSD-F12, LPNO-CCSD-F12
- Mukherjee Mk-LPNO-MRCCSD(T)
- Powerful iterative configuration expansion (ICE-CI) approximation to Full-CI
- ICE-CI for large active space CASSCF calculations
- MREOM-CCSD (also with SOC)
- Fully internally contracted MRCI
- Full TD-DFT energies and gradient for hybrid functionals
- Super-fast approximate TD-DFT: sTDA/sTDDFT of Grimme and co-workers
- PBEh-3c method of Grimme and co-workers
SCF, DFT and Hessian:
- Large performance improvements for calculations with four center integrals
- Improved performance with RI-J with conventionally stored integrals
- Gradient for range separated hybrids
- Gradient for range double hybrid functionals with meta GGAs
- Gradient for range double hybrid functionals with range separated functionals
- Gradient for RI-JK
- Frequencies for range separated functionals
- Stability analysis and automatic search for broken symmetry states
- Local spin analysis
- Fractional occupation number analysis (FOD) for detection of MR character
- All improvements for DLPNO methods as listed above
- Closed shell EOM-CCSD energies
- Closed shell STEOM-CCSD energies
- Automatic closed shell STEOM-CCSD active space selection
- EOM-CCSD(2) and STEOM-CCSD(2) approximations
- EOM-CCSD transition moments
- EOM/STEOM-CCSD core level excited states
- IP-EOM-CCSD and EA-EOM-CCSD
- ADC(2) and CC(2) methods (initial implementation)
- COSX for EOM-CCSD and STEOM-CCSD
- Improved automatic frozen core handling
- Core-correlation in automatic basis set extrapolation
- RHF/UHF CISD
- RHF/UHF CCSD
- ROHF CISD
- ROHF CCSD
- FIC-MRCI, CEPA/0 variant and DDCI3
CASSCF, NEVPT2 and MRCI
- Detailed tutorial showing CASSCF/NEVPT2 usage
- Accelerated CI (ACCCI) a more efficient CI step for multi-root calculations
- Automatic implementation of AbInitio ligand-field theory
- Simplified generation of double-shell orbitals
- Active space protection scheme and improved warnings
- ICE-CI as CI solver for larger active spaces
- Partially Contracted NEVPT2 with and without RI
- Updated interface to BLOCK 1.0
- DMRG-NEVPT2 for active spaces up to 20 orbitals
- Magnetization and magnetic susceptibility
- Printing of the wavefunction in terms of CSFs and spin-determinants
- MREOM-CCSD (also with SOC)
- Local spin analysis for CASSCF
- Fragment decomposition of the spin-spin interaction
- Cumulant approximation for NEVPT2
- ACCCI as CIStep for FIC and DLPNO-NEVPT2
- Explicitly correlated RI-FIC-NEVPT2 (NEVPT2-F12)
TD-DFT and ROCIS:
- Full TD-DFT for hybrid functionals
- Gradient for full TD-DFT with hybrid functionals
- TD-DFT/TDA gradient with range separated functionals
- ROCIS magnetic properties (hyperfine, g-tensor, ZFS tensor, MCD)
- ROCIS-RIXS spectra
- PNO-ROCIS for spectacular performance improvements
- Super-fast approximate TD-DFT: sTDA/sTDDFT
- Natural transition orbitals in TD-DFT and ROCIS
- GIAO implementation for NMR chemical shifts. Various aproximations (RIJOCOSX, RIJK)
- New Handling of basis set names. Now fully consistent with TurboMole def2-defaults (including ECPs) SARC basis sets separately available
- New reading of basis sets and ECPs together
- New correlation consistent basis sets added
- New SARC basis sets for the lanthanides; good for correlated calculations
- New ANO-RCC basis sets added
- Improved frozen core handling in correlation calculations
- Improved automatic auxiliary basis set generation
- Corrections for low-frequency modes in thermochemistry
- New and improved NBO interface
- CPCM and improved SMD solvent models
- Intrinsic atomic orbital (IAO) and bond orbital implementation
- Improved performance in Boys localization
- Updated and improved mapspc program
- Atomic Mean Field (AMFI) spin-orbit coupling operators
- EPRNMR works with range separated hybrid functionals
- New molecular dynamics module
Well it is March 14 which means it is Pi day! And to celebrate this notable scientific number developers from around the world have teamed up for a unique 10-day promotion.
Pi Fest is offering a range of scientific applications with major savings. The applications range from reference management to data analysis to electronic lab notebooks. So why not pop over and take advantage.
Chirys View is a simple molecular spreadsheet for Mac OSX. It has been designed as a fast viewer for collections of molecules represented as an SDF file (Structured Data Format). On import molecular weight, exact mass, molecular formula, hydrogen bond acceptor and donor counts are automatically calculated. You can combine multiple SDF files by multiple file imports or by coping and pasting from one document into another. You can then save selected compounds as new SDF file.
I imported 1 million structures from ChEMBL and whilst it took a few minutes to load and used 27GB RAM it did so without complaints, scrolling down a list of a million compounds is a little impractical but list sorting is pretty responsive. I had a look at some of the more complex structures and they molecular layout seems excellent and clearly legible.
As a simple molecular selection tool Chirys View works very well. My only complaint is that when you import 3D structures (e.g. from a docking run) the structures can be difficult to discern (see below), it would be nice to have a convert to 2D option.
Most drug-like molecules contain a number of rotatable bonds and prediction of bioactivities, docking etc. require an understanding of conformation. Whilst systematic methods can in theory explore all conformational space, however as the number of rotatable bonds increases a systematic search becomes prohibitive both in terms of the computational cost in generating conformations but also the time taken to process all the generated conformations (e.g. dock into protein). Thus there is great interest in rapid means to generate ensembles of representative conformations.
A recent paper DOI helps to address the problem by compiling a high quality dataset of structures generated using ligands from the Protein Data Bank.
The datasets were applied to benchmarking seven freely available conformer ensemble generators: Balloon (two different algorithms), the RDKit standard conformer ensemble generator, the Experimental-Torsion basic Knowledge Distance Geometry (ETKDG) algorithm, Confab, Frog2 and Multiconf-DOCK. Substantial differences in the performance of the individual algorithms were observed, with RDKit and ETKDG generally achieving a favorable balance of accuracy, ensemble size and runtime.
The dataset is freely available for download http://www.zbh.uni-hamburg.de/?id=628
I've just added a review of MOEsaic, this is a web service application that is part of the MOE install from Chemical Computing Group.
MOEsaic is a browser-based application for analyzing series of small molecule chemical structures and related property data (e.g. from medicinal chemistry projects). Once structure-property data is uploaded to the server, MOEsaic allows users to perform structure based searching and data analysis.
There is a complete listing of reviews here.
What do the following have in common.
They are all representation of the well known chemical Aspirin.
Structure representation, including the electronic storage of structures and reactions to enable effective information searching, retrieval and display, has become more challenging as the number, diversity and complexity of structures which can be elucidated has increased over time. This meeting will explore current and future challenges and possible solutions to overcome them. In addition, subject matter experts will anticipate how developments in these areas will bring opportunities and benefits to research and innovation in the future.
Chemical Structure Representation: What Would Dalton Do Now. 22 June 2017 10:00-16:30, Liverpool, United Kingdom Full details of the meeting
PerkinElmer have announced that their iOS apps have been withdrawn.
Although PerkinElmer Informatics remains committed to making ChemDraw available to chemists everywhere, the iPad iOS apps ChemDraw, Chem3D and CDSL have been withdrawn from the Apple iTunes store effective immediately. The related Flick2Share capability is also withdrawn from service.
Whilst it was reported that there were plans to build an Android version in 2014 nothing has seen the light of day. It seems they are now focusing on ChemDraw Cloud.
If you already have ChemDraw or Chem3D installed they will continue to operate but the "flick2share" option will not function, it is unlikely that existing apps will be updated or supported in the future.
Alternatives for Chemical Drawing
There are a number chemical drawing apps alternatives to ChemDraw under iOS on the MobileScience Website. Perhaps the most popular is ChemDoodle Mobile and is provided to you for free when you purchase ChemDoodle desktop.
There are five main windows: Draw, 3D, Calculate, Spectra and Help. The Draw window shows a typical ChemDoodle sketcher, where you can draw and store your structures. The 3D window allows you to view the drawn molecule in 3D. The Calculate page calculates properties and the Spectra page simulates NMR spectra. All spectra are interactive.
Elemental is a free chemical drawing app from Dotmatics. This is actually the same chemical sketching application provided for all the Dotmatics products and as is used for drawing chemical queries in ChemSpider. It is also used int ElementalDB an iPad app that demonstrates substructure searching the 1.2M structure ChEMBL database locally on your iPad.
Molecule is a simple modern chemical structure editor. Allow to draw and share chemical structure. MF, MW, Monoisotopic Mass and Elemental Composition calculated interactively during drawing.
MolPrime+ is a chemical structure drawing tool based on the sketcher from the Mobile Molecular Datasheet from Molecular Materials Informatics, Inc. It provides a way to view and edit chemical structure diagrams on an iPhone, iPod or iPad. The unique and innovative sketcher is optimized for the touchscreen interface, and allows professional quality molecular structures to be drawn quickly and efficiently. The same drawing tool has been used in the Green Lab Notebook.
iMolecular Draw is an application that can view, edit and build molecules in 2D.
Chirys Draw chemical drawing app for publication-quality molecular structures and reactions. Designed from the ground up for the iPad, Chirys Draw takes advantage of unique multi-touch capabilities to make drawing molecular structures and reactions easy and accurate.
I just noticed that a new version of ChemDraw has been released.
ChemDraw and ChemOffice 16.0.1 provides a point release to address a number of usability concerns, primarily on Mac, identified subsequent to the 16.0 release. ChemOffice Pro, ChemDraw Pro, ChemDraw Prime and the ChemDraw Active-X control (CDAX) have been updated.
I have no details on what issues have been addressed, hopefully the topic on the Cambridgesoft forum will provide more user experience.
OpenEye have announced the release of OpenEye Toolkits v2017.Feb. These libraries include the usual support for C++, Python, C#, and Java.
EXAMPLE NEW FEATURES
FastROCS TK now allows customization of starting points for shape overlap optimization.
Quacpac TK now includes a flexible molecular charging engine.
OEMedchem TK now allows MCS similarity scores to be computed for a query molecule compared to a set of indexed target structures.
I just noticed that the AppleScript Library Myriad Tables has been updated, Myriad Tables Lib is an AppleScript script library that gives AppleScript scripts the ability to show dialogs containing tables. It requires OS X 10.10 or later. This is just one of the great resources available from Mac OS X Automation
- ASObjC Runner is a scriptable faceless background helper application. It has a dictionary with a range of commands focused on the areas where vanilla AppleScript comes up short. You use it like a scripting addition, except you address the commands to the application. It provides better string handling (e.g. change case, encoding URL’s, regular expression, formatting dates), list sorting and filtering, improved file handling and progress dialog boxes.
- ASObjCExtras is a free framework that fills in some of the gaps in AppleScriptObjC support, as well as providing some useful extra facilities including methods for efficiently processing lists and strings.
- Myriad Tables gives AppleScript scripts the ability to show dialogs containing tables.
- CalendarLib_EC an AppleScript script library for manipulating calendar events without using Calendar.app.
- DialogToolkit an ASObjC-based script library for showing enhanced dialogs.
- Myriad Helpers is a collection of Objective-C files that simplify some of the coding involved in AppleScriptObjC.
In addition there is also Everyday AppleScriptObjC the absolutely essential guide for anyone who wants to explore the full power of AppleScriptObjC.
For more information have a look at the AppleScript Resources Page.
Chemical Computing Group have announced and update to MOE. The MOE 2016.0802 update contains a number of updates to the biomolecule modelling including improved hydrogen bond detection, and addition of a number of unnatural amino acids.
There have also been improvements to MOE/Web MOE/web. The MOE/web version compatibility check has been broadened. MOE/web license waiting has been improved. HTTPS authentication proxy server support has been improved.
Apple have announced the date and venue for the 2017 World Wide Developers Conference. WWDC will take place June 5-9, 2017 at the McEnery Convention Center in San Jose, California, USA.
Registration opens Monday, March 27 at 10:00 a.m. PDT. The opportunity to buy tickets to WWDC17 will be offered by random selection. To register, you must be a member of the Apple Developer Program or Apple Developer Enterprise Program. Tickets sell out very quickly so put an alert in your calendar now.
GROningen MAchine for Chemical Simulations (GROMACS) is a molecular dynamics package mainly designed for simulations of proteins, lipids and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers worldwide. GROMACS is one of the fastest and most popular software packages available,and can run on central processing units (CPUs) and graphics processing units (GPUs). It is free, open-source software.
These release notes document the changes that have taken place in GROMACS since the initial version 2016 and subsequent patch releases, to fix known issues. It also incorporates all fixes made in version 5.1.4 and several since.
The documentation gives details of installation.
The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. TINKER has the ability to use any of several common parameter sets, such as Amber (ff94, ff96, ff98, ff99, ff99SB), CHARMM (19, 22, 22/CMAP), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA), Merck Molecular Force Field (MMFF), Liam Dang's polarizable model, and the AMOEBA (2004, 2009, 2013) polarizable atomic multipole force field.
The TINKER package contains a variety of interesting algorithms such as: flexible implementation of atomic multipole-based electrostatics with explicit dipole polarizability, various continuum solvation treatments including several generalized Born (GB/SA) models, generalized Kirkwood implicit solvation for AMOEBA, an interface to APBS for Poisson-Boltzmann calculations, efficient truncated Newton (TNCG) local optimization, surface areas and volumes with derivatives, free energy calculations via the Bennett Acceptance Ratio (BAR) method, normal mode vibrational analysis, minimization in Cartesian, torsional or rigid body space, symplectic RESPA multiple time step integration for molecular dynamics, velocity Verlet stochastic dynamics, pairwise neighbor lists and splined spherical energy cutoff methods, particle mesh Ewald (PME) summation for partial charges and polarizable multipoles, a novel reaction field treatment of long range electrostatics, fast distance geometry metrization with better sampling than standard methods, Elber's reaction path algorithm, potential smoothing and search (PSS) methods for global optimization, Monte Carlo Minimization (MCM) for efficient potential surface scanning, tools for fitting charge, multipole and polarization models to QM-based electrostatic potentials and more....
TINKER 8 is a major new release of the Ponder Lab tool set for molecular mechanics and dynamics calculations. An important change in this new version is the switch from old-style common blocks to Fortran modules. Use of modules and greatly increased use of dynamic memory allocation means TINKER can now support very large molecular systems. TINKER 8 also implements improved OpenMP parallelization throughout many parts of the code. Additional big improvements include parallel neighbor list building and updating, and big reduction in iteration needed to converge AMOEBA polarization via an efficient PCG solver. Other changes from the previous TINKER version include new and updated force field parameter sets and numerous minor additions and bug fixes, many of them suggested by users of the package. Please note that as with prior new releases, version 8 is neither backward nor forward compatible with earlier versions of TINKER. In particular, older versions of parameter files should not be used with TINKER 8 executables and vice versa.
Learning MacroMols VR is a mobile app where you can experience macromolecules such as DNA, RNA, carbohydrates and protein structures (from the PDB – Protein Data Bank) in a virtual reality, using Google Cardboards.
It allows the viewer to explore DNA, RNA, Carbohydrates and Proteins.
EduChem VR (http://educhem-vr.com), create immersive virtual reality world of atoms and molecules, while playing. All molecules are 3D objects and one very efficient way to learn more and deeper about atoms and bonds is by VR.
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.
Download InChI version 1 (software version 1.05) for Standard and Non-Standard InChI/InChIKey (27 January 2017)
This package contains InChI Software version 1.05 (January 2017) final release.
In this version:
- support for chemical element numbers 113-118 was newly added;
- experimental support of InChI/InChIKey for simple regular single-strand polymers was implemented;
- experimental support of large molecules containing up to 32767 atoms was added;
- ability to read necessary for large molecules input files in Molfile V3000 format was added;
- provisional support for extended features of Molfile V3000 was added;
- InChI API Library was significantly updated; in particular, a novel API procedure for direct conversion of Molfile input to InChI has been added; a whole new set of API procedures for both low and high-level operations (InChI extensible interface, IXA) has been added;
- the source code was significantly modified in order to ensure multi-thread execution safety of
- the InChI Library; several minor bugfixes/changes were made and several convenience options were added to the inchi-1 executable.
Chembench is a web-based tool for QSAR (Quantitative Structure-Activity Relationship) modeling and prediction. Chembench doesn't require any programming or scripting knowledge to use. It's an interface that lets you skip past the hassles of file management and translating between programs, so you can focus on the science of making and applying predictive models. DOI.
It includes models/datasets for things like brain penetration, PGP, AMES, skin penetration etc. you can use the existing models or build your own and than evaluate novel compounds.
I've now written a couple of Jupyter notebooks and one of the issues that has come up is how to share the notebooks in a way that ensures the results will be reproducible in an environment when updates to components occur regularly.
Binder is a collection of tools for building and executing version-controlled computational environments that contain code, data, and interactive front ends, like Jupyter notebooks. It's 100% open source.
At a high level, Binder is designed to make the following workflow as easy as possible
- Users specify a GitHub repository
- Repository contents are used to build Docker images
- Deploy containers on-demand in the browser on a cluster running Kubernetes
Common use cases include:
- sharing scientific work
- sharing journalism
- running tutorials and demos with minimal setup
- teaching courses
If you want to find out more have a look at this blog post by the developers.
Maestro 11 is the portal to all of Schrödinger's computational technology – far more than just a user interface, Maestro 11 also helps researchers organize and analyze data.
I've been experimenting with the use of Jupyter Notebooks (aka iPython Notebooks) as an electronic lab notebook but also a means to share computational models. The aim would be to see how easy it would be to share a model together with the associated training data together with an explanation of how the model was built and how it can be used for novel molecules.
The Ames test is a widely employed method that uses bacteria to test whether a given chemical can cause mutations in the DNA of the test organism. More formally, it is a biological assay to assess the mutagenic potential of chemical compounds. PNAS. 70 (8): 2281–5. doi
In this first notebook a random forest model to predict AMES activity is described….
The Molecular Design Toolkit is an open source environment that aims to seamlessly integrated molecular simulation, visualization and cloud computing. It offers access to a large and still-growing set of computational modelling methods with a science-focused Python API, that can be easily installed using PIP. It is ideal for building into a Jupyter notebook. The API is designed to handle both small molecules and large bimolecular structures, molecular mechanics and QM calculations.
There are a series of Youtube videos describing some of the functionality in more details, starting with this introduction.
Every looked into the night sky and wondered what a bright object might be? If so then this is the app you need, Stellarium is a Mobile Sky Map is a fully-featured planetarium for your phone. It shows a realistic and accurate night sky map, just like what you see with the naked eye, binoculars or a telescope.
- a catalog of over 600,000 stars displayed as a real time zoomable sky map
- a catalog of many nebulae and galaxies, with pictures for some of them
- asterisms and illustrations of the constellations for several sky cultures
- artificial satellites, including the International Space Station
- realistic Milky Way
- realistic landscape and atmosphere with sunrise, sunset and light pollution simulation
- accurate simulation of stars extinction, and atmosphere refraction
- 3D rendering of the major solar system planets and their satellites
- night mode (red)
- GPS positioning, accelerometers control of the direction of view in the sky
CompTox Mobile allows the user to find chemical structure instantly by exact mass (m/z), ¹³C NMR chemical shifts, structure name or CAS Registry Number in a database of about 720,000 EPA CompTox structures.
Within the Chemistry Dashboard, users can access chemical structures, experimental and predicted physicochemical and toxicity data, and additional links to relevant websites and applications.
Just heard of a new PYMOL plugin, created by Jared Sampson, called PyMOLProbity which allows a PyMOL user to visualize MolProbity-style structural validation data directly in a PyMOL session. PyMOLProbity is a plugin allows the user to produce MolProbity-style visualization of atomic interactions within a structure (e.g. H-bonds, van der Waals interactions and clashes) directly within a PyMOL session.
The plugin runs local copies of several executable programs from the Richardson Lab at Duke University, authors of the MolProbity software, parses the output, and displays the results in the PyMOL viewport. There are both a graphical user interface (GUI) for general point-and-click use, and a command-line interface (CLI) suitable for scripting.
Chen et al. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallographica D66:12-21 DOI.
The Reduce, Probe, and Prekin executables are only available for Linux and MacOS, PYMOL is available from Schrödinger and also available via Homebrew, you will need to install XQuartz first.
There are detailed instructions on how to install a variety of chemistry/cheminfomatics/biology packages on a Mac here.
Too often I come across datasets that Chemical names or identifiers but no actual molecular structure, recently Dan at Dotmatics suggested I look at OPSIN. There are also several web services for converting names to structure and I've highlighted a couple of options here and described three scripts that allow them to be used from within Vortex.
There are many more scripts on the Hints and Tutorials Page.
A new version of SeeSAR is now available for download.
Version 5.5 includes several new features and has undergone some tweaks under the hood to improve speed.
From the release notes:-
2D browsing featuring in-view molecule properties
To further enhance the 2D browsing, we have added an illustration of the molecules' key properties in the form of a radar plot. A thumbnail of the plot is embedded in each of the 2D molecule pictures, providing a quick overview. it enlarges upon mouse-over and provides access to the configuration dialog. Add or remove property-axes, optionally fine-tune the scales and set 'desired' value ranges. A hit or miss of the latter is indicated by green or red dots on the corners of the color-coded characteristic shape of the molecule on the plot (the greener the better).
Detecting novel/unoccupied binding sites
Now SeeSAR can search your protein for unoccupied pockets based on the world-renown DoGSite-Algorithm. You may then select these to become the binding site, within which to generate poses and calculate binding affinities for your molecules. The new binding site definition feature lets you either use a selected molecule from the table (based on a 6.5Å shell around it, as before) or will detect and visualize empty pockets for you to select instead.
Multiple reference molecules
The reference molecule in SeeSAR always stays in view even when you select other entries from the molecule tables. Now, however, you are able to set - and keep in view - as many reference molecules as you like. Either set them individually - in the selected molecule menu (as before) - or mark several as favorites and set them all as references at once, via the new menu button below the table.
Multiple core replacements with just one click
With the new multiple solutions button for ReCore in the molecule editor, brainstorming new scaffold ideas became yet easier. You can now generate 10 new alternative core replacements at once. The new molecules are saved directly to the table so that you can immediately see their estimated binding affinity and view all structures in 2D at a glance.
I just came across Simply Fortran includes the GNU Fortran compiler, an advanced development environment including project management, and an integrated debugger for fast and easy installation.
Simply Fortran is tested on OSX Snow Leopard through macOS Sierra.
Added to the Fortran on a Mac page.
According to a report by Greenpeace a number of tech companies are making great efforts towards use of renewable energy, with Apple and several other companies aiming for 100% renewable energy.
Apple has “played a catalytic role within its IT supply chain, pushing other IT data center and cloud operators who help deliver pieces of Apple’s corner of the internet to follow their lead in powering their operations with renewable energy.”
It is interesting to compare the situation with the music streaming services, iTunes gets a final grade of A, whilst Pandora, SoundCloud, Spotify have grades of F or D. It is similar with the Video streaming companies, whilst YouTube gets an A, Netflix, Vevo, Vimeo and Hulu all languish with F or D.
Many of these companies are major drivers for energy use in the tech sector and this is only going to increase.
The energy footprint of the IT sector as a whole is currently estimated to consume 7 percent of global electricity, with an anticipated threefold increase in global internet traffic by 2020.
A new chemical drawing app SketchEl2 has been released.
It is based on the an original java app but as the author notes.
Although a few holdouts may disagree, Java is not the platform of the future for the desktop (that ship sailed a long time ago).
So the new version SketchEl2 is now a web runtime app built using the Electron Framework) and Node.js and the Chromium web browser.
I can't remember seeing this mentioned but if you are using a Terminal window on the new MacBook Pro with a Touchbar, if you type
the Touchbar illuminates as shown below, if you then touch "obabel" it opens the manual page for you in another window.
Seems to work for other command line tools also.
Just got this email
I am glad to announce the release of OSRA 2.1.0. OSRA (Optical Structure Recognition Application) is a tool for converting images of molecules into SDF, SMILES and many other chemical formats. Images can be pictures of single molecules or complete PDF documents with multiple pages of text and graphics. In addition to molecules OSRA can also recognize reactions, and, starting with this version, simple polymers.
The improvements in this version: - Significantly improved recognition of PDF documents, no longer dependent on Ghostscript at runtime. - Recognition of polymers (different approach from POSRA - a separate tool focused on polymer recognition).
The new version is available at osra.sf.net
Please note that if you are building from source the dependencies have changed. OSRA now requires poppler (version 0.41) to process PDF files and a custom-patched version of OpenBabel to save polymer MOL and SDF files. The patched version of OpenBabel is provided at the above url. OSRA no longer requires Ghostscript to be installed.
I just had a quick look at the server logs to get a view on the Macinchem website usage.
There were 63,000 visitors to the site of which 25% returned to the site on multiple occasions, the visitors came from 186 different countries with the US, UK and Germany topping the listings.
The most viewed pages were
- Chemical Drawing
- Fortran on a Mac
- Cheminformatics on a Mac
- Data Analysis Tools
- Clipboard Managers
- Software Reviews
- Hints and Tutorials
- Applescript and curl
- Scientific Applications under Sierra
The update to Sierra proved to be mostly painless with many applications reporting "no known issues".
iBabel was downloaded 1216 times
iBabel is a GUI (graphical user interface) for the open source cheminformatics toolkit OpenBabel. It also provides an interface to a variety of tools built using OpenBabel and a molecule viewer.
Safari and Chrome were each used by around 40% of visitors, with Firefox on 14%, the once dominant Internet Explorer was below 3%. 60% of the visitors are using Mac OSX, 25% Windows and 9% OS. Looking at the last months data around 55% are using Mac OSX 10.12 and a further 28% Mac OSX 10.11 suggesting most visitors are migrating to the latest version of the operating system promptly.