bio-scaffold-analysis
Analyzes chemical libraries by scaffold using Bemis-Murcko scaffolds, generic frameworks, cyclic skeletons, matched molecular pair (MMP) analysis via mmpdb, R-group decomposition, Free-Wilson analysis, scaffold hopping, and chemotype-aware ML train/test splits. Use when identifying chemotype clusters in a library, deriving SAR transformation rules, decomposing series into R-groups, performing scaffold-balanced QSAR splits, or planning analog campaigns.
npx skills add BioTender-max/awesome-bio-agent-skills --skill scaffold-analysis --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## 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>` then `help(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
- Version Compatibility
- Scaffold Representation Taxonomy
- Library Chemotype Clustering
- Bemis-Murcko Scaffold Split (ML)
- R-Group Decomposition
- Matched Molecular Pair Analysis (MMPA) via mmpdb
- Context-Based MMPA
- Scaffold Hopping
- Series Detection
- Per-Tool Failure Modes
- Bemis-Murcko -- linear molecule yields empty
- Bemis-Murcko -- spiro / bridged ring confusion
- Generic framework -- loses heteroatom info
- Scaffold split -- imbalanced classes
mmpdb fragment data.smi -o data.fragments mmpdb index data.fragments -o data.mmpdb mmpdb transform --smiles 'COc1ccccc1' --property pIC50 data.mmpdb
What does the bio-scaffold-analysis skill do?
Analyzes chemical libraries by scaffold using Bemis-Murcko scaffolds, generic frameworks, cyclic skeletons, matched molecular pair (MMP) analysis via mmpdb, R-group decomposition, Free-Wilson analysis, scaffold hopping, and chemotype-aware ML train/test splits. Use when identifying chemotype clusters in a library, deriving SAR transformation rules, decomposing series into R-groups, performing scaffold-balanced QSAR splits, or planning analog campaigns.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill scaffold-analysis --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.