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Trying to squeeze sense out of chemical data

Archive for the ‘shape’ tag

Conformational Envelopes

without comments

Joe Leonard posted a question on the CCL mailing list today regarding “conformation envelopes”. More specifically, he asked

Has there been work on creating visualizations of “conformer envelopes”, graphical representations of the conformational space occupied (or available) to molecules. Particularly when such visualizations are used to (quickly/visually) compare whether 2 molecules can adopt the same shape – or if there are shapes of one that can’t be adopted by another.

A while back when I was investigating the use of the Ballester & Graham-Richards shape descriptors for 3D similarity searching. It turns out they perform quite poorly in enrichment benchmarks (which I’ll describe in a future post). At that time I was thinking of how Pub3D could scale to a multi-conformer version and I realized that the shape descriptors would allow me to easily visualize the “shape space” of a set of compounds. When these compounds are conformers for a molecule, one effectively gets a conformational envelope.

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Written by Rajarshi Guha

November 8th, 2008 at 10:49 pm