Computational Chemistry Tools

Computational Chemistry can have a major impact on all stages of the drug discovery process, whether it be providing small desktop tools to enable scientists to access information more easily (See ChemSpider Safari Extension), calculation of physicochemical properties, virtual screening, structure-based design, QSAR analysis of both the desired target but also off-target activities.

There are a huge number of tools available, ranging in price from free to many $100,000s, here I’ll describe some of the tools I have used so whilst it is not comprehensive it might provide a useful stating point.

Work In Progress!! Much more to come.

ChemAxon

ChemAxon provide a number of desktop tools such as the drawing tool Marvin but also provide plugins to calculate a variety of physicochemical properties. In particular a tool to calculate pKa and the resulting LogD, probably the most important physicochemical property in medicinal chemistry. There are command line versions of these calculations that are invaluable for dealing with very large data-sets. I’ve written a review of Marvin here.
LibraryMCS is a tool from ChemAxon that uses hierachial clustering to sort molecules based on maximum common substructure, I find this an invaluable tool for looking at HTS data and is complimentary to other descriptor based clustering tools, an example can be found on the analysis of the Malaria screening.

Chemical Computing Group

MOE (Molecular Operating Environment) is my main Computational Chemistry tool and it provides nearly all the functionality required for drug discovery. MOE is a software system designed to support Cheminformatics, Molecular Modelling, Bioinformatics, Virtual Screening, Structure-based-design. I’ve written a couple of reviews of MOE here.

In addition the SVL scripting language also provides a powerful means to extend the capabilities of MOE and to build new tools. SVL Exchange, a repository of programs and code samples written in the Scientific Vector Language (SVL) by users and developers of the Molecular Operating Environment. The SVL Exchange is a valuable resource for users seeking specialized applications, utilities, or customizations for MOE. For users who program in SVL, the files in the SVL Exchange can also serve as examples of SVL programming. An example of the use of SVL can be found on the analysis of the Malaria screening where the two result sets were compared using a SVL script (db_nb_mols_incommon) that identifies identical compounds in multiple databases, showing there were 49 identical compounds in the two results sets.

LigandScout

Dotmatics

Examples of tools in use.


Updated 25 July 2010
See Also computational chemistry books.

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