bio-scaffold-analysis
Version Compatibility
Reference examples tested with: RDKit 2024.09+, mmpdb 3.1+, scikit-learn 1.4+, datamol 0.12+.
Before using code patterns, verify installed versions match. If versions differ:
- Python:
pip show <package>thenhelp(module.function)to check signatures
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
Scaffold Analysis
Analyze chemical libraries by their underlying scaffolds. Bemis-Murcko (1996) is the canonical scaffold decomposition: ring systems + linkers, with all R-groups stripped. Generic framework + cyclic skeleton are progressively-more-abstract views. Scaffold analysis underpins QSAR train/test splits (preventing data leakage), library diversity assessment, chemotype clustering, R-group decomposition for SAR modeling, and matched molecular pair analysis (MMPA). The choice of scaffold representation determines whether two compounds are "the same series" -- a critical decision for medicinal chemistry workflows.
For reaction-based enumeration and Free-Wilson, see chemoinformatics/reaction-enumeration. For scaffold-hopping via fingerprints, see chemoinformatics/similarity-searching. For 3D shape-based scaffold hopping, see chemoinformatics/shape-similarity.