5 ms·
Right, it's not technically difficult to match a scaffold -- you can probably parallelize a big RDKit job, but it's nontrivial to scale to a gigascale set. And,
by whymauri 5y ago
Right, it's not technically difficult to match a scaffold -- you can probably parallelize a big RDKit job, but it's nontrivial to scale to a gigascale set. And, like you mentioned, there's rule-based substructure matching (sometimes easier for those willing to venture a bit outside SMILES). Anyways, it was more a curiosity question -- thank you for the details on Lufotrelvir!
- dekhn 5y agoyou wouldn't run a big rdkit job, you'd just featurize all your molecules and then do vector comparisons. lots less CPU but a big risk of false negatives.
- whymauri 5y agowhat does 'featurize' mean here? do you mean fingerprint feature vectors? IIRC, the computation time to get a fingerprint vector vs. extracting a murcko scaffold are pretty similar, although it depends on the fingerprint.