autodock-vina-docking SKILL.md skillA
autodock-vina-docking from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/autodock-vina-docking@git:20260428.81ea2d2Pins git:20260428.81ea2d2 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/structural-biology-drug-discovery/autodock-vina-docking/SKILL.md- Versions recorded
- 2
- Latest version
- git:20260428.81ea2d2, committed Apr 28, 2026
- First version recorded
- Feb 18, 2026
- Size
- 15,860 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
Molecular docking with AutoDock Vina (Python API). Receptor/ligand prep (Meeko + RDKit), grid box, docking, pose and binding energy analysis, and batch virtual screening.
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
# AutoDock Vina Molecular Docking ## Overview AutoDock Vina is one of the fastest and most widely used open-source molecular docking engines for predicting protein–ligand binding modes and affinities. This skill covers the full Python-based pipeline: receptor preparation from PDB, ligand preparation from SMILES/SDF via Meeko and RDKit, search box definition, docking execution, pose analysis, and batch virtual screening for hit identification. ## When to Use - Predicting binding poses of small molecules to a protein target - Estimating relative binding affinities (kcal/mol) for ligand ranking - Virtual screening of compound libraries against a target receptor - Validating docking protocols by re-docking co-crystallized ligands - Preparing docking inputs from SMILES strings without intermediate files - Comparing binding modes of analogs in a structure-activity relationship study - Generating starting poses for molecular dynamics simulations - Use **DiffDock** instead for blind docking when the binding site is unknown; use **GNINA** as an alternative with CNN scoring ## Prerequisites …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/autodock-vina-docking@sha256:903c577e3265fff7The line at the top of this page pins the label git:20260428.81ea2d2, 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_e5fits773znd3pwa)
1 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 2 versions of this file, between Feb 18, 2026 and Apr 28, 2026, about one every 69 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260428.81ea2d2 latest | 2026-04-28 | 81ea2d2 | 15,860 B | A | view · diff |
| git:20260218.8df1694 | 2026-02-18 | 8df1694 | 15,948 B | A | view |
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 (15860 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
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_e5fits773znd3pwa GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/autodock-vina-docking GET https://markdownregistry.com/api/v1/blob/903c577e3265fff7e8a634f97353aa57386e1a32edabba75207e52709ea93d44
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.
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