bio-covalent-design skillA
bio-covalent-design is agent-read markdown (skill) from pku-yuangroup/openai4s: Designs covalent inhibitors and warheads targeting cysteine, lysine, serine, threonine, tyrosine, and aspartate residues, with explicit handling of warhead reactivity (acrylamide, chloroacetamide, vinyl sulfone, sulfonyl fluoride, fluorosulfate, aldehyde, boronate, nitrile), reversibility (kinact/Ki, t_residence), glutathione (GSH) stability, intrinsic reactivity assays, and covalent docking (DOCKovalent, GOLD, HCovDock). Use when designing covalent inhibitors for targeted covalent inhibition (T.
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: RDKit 2024.09+, OpenEye / AutoDock Vina 1.2+ (for covalent extensions), GOLD (commercial), DOCKovalent (web service), HCovDock 1.0+. Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show rdkit` then `help(rdkit.Chem)` to check signatures - CLI: check version output of each docking tool If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Covalent Inhibitor Design Design molecules that form covalent bonds with target protein residues. Clinically validated targeted covalent inhibitors include KRAS G12C inhibitors (sotorasib, adagrasib), BTK inhibitors (ibrutinib), and EGFR inhibitors (osimertinib). Covalent design requires balancing **intrinsic reactivity** (must form bond) vs **selectivity** (only the intended residue), **reversibility** (irreversible vs reversible covalent), and **drug-likeness** (warheads can hurt PK). …
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How to install
mdr add pku-yuangroup/openai4s/bio-covalent-design@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-covalent-design@sha256:5265d1ef1edeeebbPin 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_nfyrb5i3fqomtu25)
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Audit of the latest version
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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_nfyrb5i3fqomtu25 GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-covalent-design GET https://markdownregistry.com/api/v1/blob/5265d1ef1edeeebbf59645829bd969563859274d5487e3f653873811a4dbe0e3
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