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Problem: The Bayer set contains large flexible drug molecules that range from 12-30 heavy atoms. Current fingerprint & clustering methods result in 525 molecules & 16,242 conformers. We need to reduce data set to ~3 conformers/molecule.
Hypothesized contributors to large number of conformers:
Large molecule size
Excessive rotatable bonds
Approach:
After I get a reasonably sized set of optimized molecules (through a size filtering method or rotatable bond filtration), I will submit these.
I will use Fragmentation as a second data set iteration or if I am unable to achieve 3 confs/mol in step 1. I will report how fragmentation affects conformer generation. I hypothesize this will reduce # of conformers because smaller resulting molecules.
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