bio-protac-degraders skillA
bio-protac-degraders is agent-read markdown (skill) from pku-yuangroup/openai4s: Designs PROTACs, molecular glues, and bivalent degraders with explicit handling of E3 ligase choice (VHL, CRBN, IAP, MDM2, KEAP1), linker design (length, composition, rigidity), ternary complex prediction (PRosettaC, DeepTernary, AlphaFold3), cooperativity (alpha), DC50 / Dmax characterization, hook effect, and prediction-experiment reconciliation. Use when designing targeted protein degraders, planning linker SAR, predicting ternary complex stability, or building generative degrader workflows..
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: PRosettaC (web service), DeepTernary research code, AlphaFold3, Boltz-1 / Boltz-2, RDKit 2024.09+, OpenMM 8.1+ (for ternary MD). 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. # PROTAC and Bivalent Degrader Design Design bifunctional molecules (PROTACs) that recruit an E3 ubiquitin ligase to a target protein, inducing target ubiquitination and proteasomal degradation. PROTACs differ from traditional drugs: a productive **ternary complex** (target + PROTAC + E3) is required, not just target binding. The modality has produced clinical programs, but their development and regulatory status changes rapidly and must be checked from current sources. PROTAC design balances **target ligand binding**, **E3 ligand binding**, **linker geometry** (length, rigidity, chemistry), **cooperativity**, **dose-dependent ternary-complex formation**, and **cell… …
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How to install
mdr add pku-yuangroup/openai4s/bio-protac-degraders@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-protac-degraders@sha256:c9fb1bb7d9cbf06fPin 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_ben6h7azjj4r4rkt)
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Source
pku-yuangroup/openai4s · 586 stars · license MIT · pushed 2026-09-23 · branch main
API
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