bio-ml-docking-rescoring SKILL.md skillA
bio-ml-docking-rescoring from pku-yuangroup/openai4s is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add pku-yuangroup/openai4s/bio-ml-docking-rescoring@git:20260821.2d1b678Pins git:20260821.2d1b678 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- pku-yuangroup/openai4s
- Path
skills/bioskills/bio-chemoinformatics-ml-docking-rescoring/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 17,353 bytes
- Repository stars
- 662
- License
- MIT
Performs ML-based protein-ligand pose prediction and scoring using DiffDock-L (diffusion-based), Boltz-1 / Boltz-2 (foundation model with affinity), Chai-1, AlphaFold3 ligand, EquiBind, TANKBind, NeuralPLexer, and hybrid workflows (DiffDock pose + GNINA rescore + PoseBusters QC). Explicit handling of when ML beats classical docking, when classical beats ML, the PB-invalid pose problem, and rescoring as the standard production hybrid. Use when modern docking is needed: foundation-model…
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
## Version Compatibility Reference examples tested with: DiffDock-L (Corso et al. 2024), Boltz-1 1.0+, Boltz-2 (Passaro et al. 2025), Chai-1 0.4+, AlphaFold 3 (DeepMind), EquiBind, TANKBind, GNINA 1.1+, and PoseBusters 0.6+. Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `diffdock --version`; `boltz --version` If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # ML Docking and Rescoring Use machine-learning models for protein-ligand pose prediction and affinity scoring. Foundation models such as AlphaFold 3, Boltz, and Chai-1 handle protein-ligand complex prediction, while DiffDock-L extends the original DiffDock method for ligand-pose sampling (Corso et al. 2023, 2024). Boltz-2 reports affinity prediction approaching physics-based free-energy methods on its evaluated benchmarks at substantially lower computational cost. Physical plausibility remains a separate requirement: on the PoseBusters Benchmark, the original DiffDock produced a correct and… …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-ml-docking-rescoring@sha256:79905b35c77f5a82The line at the top of this page pins the label git:20260821.2d1b678, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_jqo3z7fta263vvrj)
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Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (17353 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_jqo3z7fta263vvrj GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-ml-docking-rescoring GET https://markdownregistry.com/api/v1/blob/79905b35c77f5a820813ecc7d7ad5acff944e0c534ce73e979a47db42c0e22aa
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.