A question for computational/medicinal chemists working in drug discovery: In your day-to-day work, which computational tools/programs (small or large; commercial or open source) do you find most useful? For which application(s)? Naming just one or two of your favorites would be much appreciated. Many thanks in advance!

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Jürgen Bajorath on Jun 12, 2015 • 1 answer
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It's always an interesting exercise to answer a question like this -- especially if one uses a fair number of different tools. After a bit of thought, I think I can narrow the list down to four programs that I find myself launching at least once (and often many times) in the course of most projects:

1) PyMol (http://sourceforge.net/projects/pymol/): in its earlier incarnations, the menu options were primitive and the command syntax was clunky, but this program has gotten increasingly friendly and I now count it as a great pal and confidante. Whereas I once only used this if I wanted to make fancy graphics, it is now my go-to tool for even the most routine structural visualization, and has an array of plug-ins and wizards that achieve exceptional analytical functionality.

2) Vega-ZZ (http://nova.disfarm.unimi.it/cms/index.php?Software_projects:VEGA_ZZ): old-school modelers might see this as a modeling environment with a feel and functionality that blends features of SYBYL and Insight-II. I am increasingly relying on Vega-ZZ for molecule building, editing, structural refinement, and conformational analysis, and have recently started making use of its molecular database functionality.

3) Weka (http://www.cs.waikato.ac.nz/ml/weka/): other users could probably suggest other data mining platforms with a greater array of supported methods for feature selection, classification and clustering, but I find that Weka is a great first step for chemoinformaticists who have realized the perils of over-fit linear regression QSAR models and are looking for an easy way to explore SAR relationships and to identify robust higher dimensional relationships.

4) PaDEL Descriptor (http://www.yapcwsoft.com/dd/padeldescriptor/): whenever I need a diverse array of molecular descriptors, this is my first choice. I realize that Dragon has a larger number of descriptors to choose from, but when it comes to using molecular features, I strongly prefer open-source. Why? Because if I can't figure out from the originating paper what a descriptor is supposed to represent, there's no better recourse than to stare at the source code for a while.

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Gerald Lushington on Jun 17, 2015
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