...
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.
Experimental notes:
Clustering method: DBSCAN eps = 0.3, min_samples = 4
Fingerprint method: MACCS (supported by previous experiments from Hyesu Jang)
Method | # of molecules | # of conformers | notes |
|---|---|---|---|
Randomized size selection | 524 | ||
Conclusion: