bio-pharmacophore-modeling skillA
bio-pharmacophore-modeling is agent-read markdown (skill) from pku-yuangroup/openai4s: Builds and applies 3D pharmacophore models using RDKit Pharm3D, the apo2ph4 receptor-based workflow (Heider et al. 2023), Pharmer / Pharmit for search, and PharmacoForge for protein-pocket-conditioned pharmacophore generation (Flynn et al. 2025), covering ligand-based pharmacophores from active-set alignment and receptor-based pharmacophores from binding-pocket geometry. Explicitly handles feature types, geometric tolerances, partial matching, and pharmacophore-based virtual screening. Use when .
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What the file says
## Version Compatibility Reference examples tested with: RDKit 2024.09+, Pharmit web service, and PLIP 2.4+ (interaction analysis). Verify the deployed Pharmit/Pharmer interface and query format before automation. Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show rdkit` then `help(rdkit.Chem.Pharm3D)` 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. # Pharmacophore Modeling Build 3D pharmacophore queries that capture the essential interaction features of a ligand-target binding event. A pharmacophore is the *spatial arrangement of pharmacophore features* (donor, acceptor, hydrophobe, aromatic, charged) sufficient for activity, abstracted from any specific chemotype. Use pharmacophores for scaffold hopping, virtual-screening prefilters, and cross-target SAR transfer. Derive interaction features directly from a co-crystal when available, use apo2ph4 to derive models from an apo pocket (Heider et al. 2023), or align known actives for a ligand-based model. PharmacoForge generates candidate 3D… …
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How to install
mdr add pku-yuangroup/openai4s/bio-pharmacophore-modeling@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-pharmacophore-modeling@sha256:a060fbd45483a963Pin 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_isb6gkvaqytpqood)
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Source
pku-yuangroup/openai4s · 586 stars · license MIT · pushed 2026-09-23 · branch main
API
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