bio-scaffold-analysis skillA
bio-scaffold-analysis is agent-read markdown (skill) from pku-yuangroup/openai4s: 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..
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What the file says
## 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. …
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How to install
mdr add pku-yuangroup/openai4s/bio-scaffold-analysis@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-scaffold-analysis@sha256:4d70f98677e2a358Pin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
[](https://markdownregistry.com/a/art_a6tr7jrkpd6jsejg)
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Source
pku-yuangroup/openai4s · 586 stars · license MIT · pushed 2026-09-23 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_a6tr7jrkpd6jsejg GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-scaffold-analysis GET https://markdownregistry.com/api/v1/blob/4d70f98677e2a3587a3959472aa8705ae858341e14267e5d1a9effbe52ed4c04
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