bio-pose-validation skillA
bio-pose-validation is agent-read markdown (skill) from pku-yuangroup/openai4s: Validates docked / generated protein-ligand poses using PoseBusters physical-validity tests, strain energy quantification, geometric checks (planarity, vdW overlap, bond/angle distortion), and pose-energy reasonableness. Use when QC-ing docking results, comparing classical vs ML docking outputs, or filtering pose lists before SAR analysis..
Indexed from public GitHub and served as immutable, content-addressed versions. Install it pinned to an exact SHA-256 with the mdr CLI, and every file is verified against the hash recorded here before it reaches your agent. The deterministic audit below grades the latest version, and the same file always earns the same grade.
What the file says
## Version Compatibility Reference examples tested with: PoseBusters 0.6+, RDKit 2024.09+, pandas 2.2+, posecheck 0.5+ (optional). 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. # Pose Validation Test docked or AI-generated protein-ligand poses for physical plausibility. PoseBusters (Buttenschoen et al. 2024) provides geometric, chemical, and energetic checks that flag implausible poses, including non-planar aromatic rings, van der Waals clashes, broken bonds, altered stereochemistry, and unfavorable internal energies. On the Astex Diverse Set, DiffDock achieved 72% RMSD success but only 47% combined RMSD-and-PB-valid success; the size of this gap is dataset- and method-dependent. PB-valid status complements RMSD for downstream SAR, FEP setup, or generative-model training. For docking, see `chemoinformatics/virtual-screening`. For ML docking specifically, see `chemoinformatics/ml-docking-rescoring`. …
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How to install
mdr add pku-yuangroup/openai4s/bio-pose-validation@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-pose-validation@sha256:7c796c1375827c65Pin 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_lr4buullr7xrthue)
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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_lr4buullr7xrthue GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-pose-validation GET https://markdownregistry.com/api/v1/blob/7c796c1375827c65c7f210d53f21373a46152db020b31ce0df7a34048209e33a
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