I’ve just added the latest script for Vortex.
In previous scripts we have generated data using a local Java program, C program, PERL script, and SVL program. In this tutorial rather than have a local application generate the data we will use a web service.
There are more scripts on the Hints and Tutorial pages.
I’m a great fan of SMILES notation (simplified molecular-input line-entry system) as a compact means of storing chemical structures, and whilst there are many tools for creating SMILES strings they often give different (but acceptable) results. Various algorithms for generating Canonical SMILES have been developed, including those by Daylight Chemical Information Systems, OpenEye Scientific Software, MEDIT, Chemical Computing Group, MolSoft LLC, all use proprietary code. In the latest issue of Journal of Cheminformatics Noel O’Boyle describes the development of Universal SMILES and Inchified SMILES as implemented in Open Babel an open source cheminformatics toolkit. DOI
Vortex is an advanced data analysis package that understands chemistry, the capabilities of Vortex can be extended by the use of scripts. I’ve now created Vortex script exchange that users can use to download or share scripts.
There are also a series of scripting tutorials here to provide a starting point for creating new scripts.
Hopefully these scripts will be valuable to you.
I just noticed ChemDoodle web components have been updated
As part of an initiative to provide computational chemistry tutorials there is a competition now on.
Details for the competition Requirements Use freely available software tools and develop tutorials & models for workflows as requested in the challenges. Criteria to Judge
- Quality of predictive models
- Statistical measures, held-out test sets
- Quality of workflows
- Are these state-of-the-art?
- Clarity of the tutorials
- Suitable for undergraduate courses
- Include principles of underlying science
- Include description of “common pitfalls”
- Include description of all preparative steps & required resource
- Ease of use of the tools
- Can they be tailored/amended if new insights emerge (project specific or general insights)?
- Innovation of the computational methods
- Challenge 1: Workflow to analyze HTS data & build models for further hit finding
- Challenge 2: Structure-based design workflow, new chemotypes
- Challenge 3: Structure-based design workflow, medicinal chemistry strategy
- Challenge 4: Call for innovative drug discovery workflows
A new version of StarDrop is now available. The new features include
- FieldAlign – this new module, using Cresset's molecular Field technology, provides a unique, 3-dimensional (3D) insight into the biological activity, properties and interactions of your compounds, helping to guide the design of novel, potent compounds with a high chance of success, there is a review of the FieldView and FieldAlign here.
- R-Group analysis – analyse a chemical series to interactively visualise the impact of variations to R-groups, linkers, atoms or fragments on compound properties. Explore the SAR of your chemistry, identify new optimisation strategies and automatically enumerate the missing combinations
- ADME QSAR – new models for predicting 2C9 pKi, BBB category and P-gp category (the old models remain available for consistency with previously calculated results)
- Nova – now available with the ability to select compounds using a combination of properties and chemical diversity
Andrew Dalke has just released fmcs-1.0. It finds a maximum common substructure of two or more structures. Some of the features are:
- handles 1,000s of structures
- several different atom and bond comparison schemes
- modifiers to require ring bonds only match ring bonds, or that incomplete rings are not allowed in the MCS
- user-defined atom class typing through isotope labels (SMILES) or through an SD tag field
- uses an exact solution to find a maximum common substructure
- eports the current best solution if the timeout is reached
The software is distributed under the 2-clause BSD license and available for no charge from https://bitbucket.org/dalke/fmcs/downloads/fmcs-1.0.tar.gz
You must have the Python bindings to RDKit in order to run fmcs.
Usage details are in the README, shown also in the project page at: https://bitbucket.org/dalke/fmcs/
forgeV10 takes advantage of Cresset’s patented ligand comparison method to align, score and compare molecules from a biological viewpoint
It is designed to
- Decipher complex SAR and communicate the results
- Design better molecules based on predictions you can trust
- Prepare detailed pharmacophores
- Virtually screen 10 000 compounds on your desktop
- Generate ADME and off target activity profiles.
I’ve just completed a review of CheS-Mapper.
CheS-Mapper (Chemical Space Mapper) is a 3D-viewer for chemical datasets of small molecules, a recent publication in the Journal of Chemiformatics describes the application DOI: 10.1186/1758-2946-4-7, In addition more information is available on the wiki page. Whilst there are many applications for the visual analysis of data, very few provide the tools needed to handle chemical structures, CheS-Mapper is a java application that runs under Mac OSX (I only tested Lion) based on the Java libraries Jmol, CDK, WEKA, and utilizes OpenBabel and R, that provides an interesting means to explore chemical data sets.
There a complete list of software reviews here.
The Mobile Molecular DataSheet (MMDS) has been updated. Two major usability enhancements:
(1) Additional tool banks on the left and right side of the sketcher provide simplified drawing tools that are more familiar to users of desktop chemical drawing software.
(2) A tooltip system provides tips, live demonstrations and links to documentation.
I recently wrote a couple of Applescripts that use the Chemical Identifier Resolver (CIR) a web service that performs various chemical name to structure conversions and it occurred to me that is should be possible to use this service to generate images for use as popups on a graph in the same way that I’ve previously described using Flot and ChemSpider. This works well but relies on the structure already being in the ChemSpider database, for novel structures we need a service for generating the image from a chemical identifier. CIR provides a simple web service for doing exactly this, for example submit a SMILES string and it can return a 2D image.
This tutorial shows how to create an interactive plot using Flot and CIR
From the KNIME newsletter
“…good news for our Mac Users! We have just released KNIME 2.5.4 which fixes issues caused by the latest Apple update of the Java environment. We are grateful to the very active KNIME community which has helped to identify and fix this problem.”
KNIME Desktop 2.5.4 can be downloaded from the download page (http://www.knime.org/download) or you can upgrade your existing KNIME installation by using the built-in update functionality available in the "File" menu
There is also a KNIME tutorial here
The SVG support in Openbabel has undergone significant improvements due to the brilliant efforts of Noel O’Boyle and Chris Morley in particular the ability to colour a substructure within a molecule. This requires installation of the development version of OpenBabel at present.
I’ve added a movie to show it in action.
MolSoft have announced the release of ICM version 3.7-2c.
New features include Atomic Property Fields APF is a 3D pharmacophoric potential implemented on a grid. APF can be generated from one or multiple ligands and seven properties are assigned from empiric physico-chemical components (hydrogen bond donors, acceptors, Sp2 hybridization, lipophilicity, size, electropositive/negative and charge).
The 3D ligand Editor is a powerful new tool for the interactive design of new lead compounds in 3D. It allows you to make modifications to the ligand and see the affect of the modification on the ligand binding energy and interaction with the receptor.
Use AQUASITES to design chemicals based on their ability to displace or keep water molecules inside the ligand binding site of proteins. The first step is to identify water binding sites and then the second step is to estimate the free energy of water displacement for a particular ligand(s).
Protein Modelling Inside ICM there are many features for homology modelling and loop modelling. This new option can be used if you have a gap in your protein and you want to find loops in the PDB which fit the gap.
"Pipe-able" Scripting in ICM. New options to pipe icm commands and scripts. Easy way to write pipe-able scripts (see $ICMHOME/molpipe/*.icm). Easy way to add parallelism to unix/mac ICM scripts: fork with pipe option ($ICMHOME\molpipe*.icm)
I’ve just added a new Vortex script, this one uses a PERL script that is part of the excellent MayaChemTools.
Scripting Vortex Using OpenBabel
Scripting Vortex 2 Using filter-it
Scripting Votrex 3 Using cxcalc
Scripting Vortex 4 Using MOE
Scripting Vortex 5 Calculating similarities using OpenBabel
Scripting Vortex 6 Filtering compounds
Scripting Vortex 7 Using MayaChemTools
This might be of interest.
Dotmatics is looking to expand the team working on Vortex, its data analysis platform. The candidate should have several years software development experience with Java and preferably with the Swing graphical user interface toolkit. The ideal candidate will have a degree or PhD in the life sciences, and will have experience with data visualisation and analysis techniques such as clustering. Experience with cheminformatics systems or statistical software, such as R, will be advantageous. Candidates will probably have experience working within the pharmaceutical/biotech sector or the life science software development industry.
The position will be based at the UK headquarters in Bishops Stortford (Herts, UK). We offer a competitive salary, benefits and a pleasant working environment at the Old Monastery site. Further information about the company and our software can be found at http://www.dotmatics.com.
Whilst Vortex has tools that allow you to do some analysis and of course you can use the scripting facility to access statistical or model building packages like R in this tutorial we will be using a model taken from the literature and implementing it within Vortex using a calculation field to construct the algorithm.
It can be downloaded from here (24MB), this version requires Mac OS X 10.6 or higher and OpenBabel 2.3
Much will seem familiar to previous users of iBabel and the screenshots of the old version give a good overview of the capabilities, whilst the images below highlight a few of the new features.
The “Add title and index” option appends a title (default is Mol, but you can edit this in the adjacent text box) and an index number to multi-molecular files, e.g. Mol 1, Mol 2, Mol 3 etc. This is essential if you want to search files displayed in the “Viewer” since you need a unique identifier for each structure. In many cases the molecules will already have a molecule id.
Another new feature with OpenBabel 2.3 is the ability to generate 2D and 3D coordinates.
Perhaps the biggest changes have come with the “Viewer”, by storing the table data in an array we can use some of the cool ObjC functions such as the continuously updating selection count and the live searching of the “Name” text field. To import records identify the input file using the input button and then click the “Import” button.
The buttons highlighted in green allow the user to delete the highlighted row, delete all the “Selected” rows or clear all records completely. The selection can be modified using the buttons highlighted in pale blue.
For the other viewers, JMOL/JChemPaint are in the application bundle. ChemBioDraw needs to be in the Application folder but only works on some machines (something to do with only supporting 32-bit which I think we will have to wait for CambridgeSoft to address). Because of Java security issues Marvin has to be in the same file structure as the htm page, I think you only need to put an alias to Marvin in the Macintosh HD:Public folder or User:Public folder. the 2D and 3D radio buttons allow you to choose an appropriate display.
It also support JME as the editor but you need to get a copy from Peter Ertl directly and put it in the Public folder.
The PChem button pulls structures from PubChem, this can either be a single structure of a list (here is an example caslist.txt you can download to try).
As you can see the list contains a mixture of systematic names, trivial names, drug names and CAS numbers but the smart people at PubChem sort all that out nicely.
The result is two files on your output.smi which contains the successful searches and NoStructure.txt which contains cases where no structure was found. You can then import the file to view the structures.
I’d be delighted to hear of any bugs (honest) any suggestions for how iBabel might be improved.
There are a number Safari Extensions described on this site that access similar services and with the help of Matt I'm happy to anounce a new addition.
The Safari Extension for Opsin (download) allows the user to highlight a chemical name in a web page and then control click affords a dropdown menu, click on "Display ... using Opsin" and a small window will open displaying the chemical structure. What is particularly nice is that in addition to providing the structure in png format the same web service also provides the chemical structure in SMILES, InChi and CML format. If you click one of the buttons and the bottom of the structure window the structure will be downloaded in the appropriate format. You can read more about this extension here.
There is a full listing of the Safari Extensions here.
A selection of extensions that should be useful for chemists.
Chemspider :- Displays structure of highlighted chemical/drug and links to ChemSpider page.
PubChem :- Search PubChem for the highlighted compound
eMolecules :- Search eMolecules for the highlighted compound
Chemicalize :- Submit the current URL to chemicalize.org
DrugBank :- Search DrugBank for the highlighted compound
- Instant JChem Personal (an new OS independent desktop application for working with chemical and non chemical data) and Marvin, a chemical editor and viewer suite are free for all users
- All products are free for academic teachers and researchers - including the enterprise edition of Instant JChem
- Most products are free for freely accessible, non commercial websites