smina-molecular-docking SKILL.md skillA
smina-molecular-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/smina-molecular-docking@git:20260528.0e69cedPins git:20260528.0e69ced 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/smina-molecular-docking/SKILL.md- Versions recorded
- 3
- Latest version
- git:20260528.0e69ced, committed May 28, 2026
- First version recorded
- May 28, 2026
- Size
- 14,751 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
smina molecular docking CLI. AutoDock Vina fork with customizable scoring functions, native SDF/MOL2/PDB ligand input, autoboxing, local energy minimization, and per-atom score breakdowns. Pipeline: receptor PDBQT prep -> ligand prep (RDKit/OpenBabel) -> dock via autobox or explicit grid -> rescore/minimize with custom scoring -> rank poses by affinity. Choose smina over Vina when you need custom scoring terms (--custom_scoring), local optimization of an existing pose (--local_only), per-atom…
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
# smina Molecular Docking ## Overview smina is an AutoDock Vina 1.1.2 fork focused on flexible scoring and minimization. Accepts SDF/MOL2/PDB ligands directly (no manual PDBQT), autoboxes from a reference ligand, ships six built-in scoring functions plus arbitrary `--custom_scoring` terms, and prints per-atom score contributions. CLI-only — drive from Python via `subprocess`. ## When to Use - Re-scoring or locally minimizing an existing pose (`--local_only`, `--minimize`) without a full search - Single-pose binding energy without docking (`--score_only`) - Docking with a custom or empirical scoring function tuned to a target class - SDF/MOL2/multi-ligand input without per-ligand PDBQT conversion - Autoboxing the grid around a co-crystallized reference ligand - Per-atom energy decomposition (`--atom_term_data`) for medchem analog design - Batch virtual screening that parallelizes well across nodes (one CLI process per ligand) - Use **autodock-vina-docking** instead when you need Vina Python bindings, Vinardo scoring, or Vina 1.2's expanded force field; use **diffdock** when the binding site is unknown ## Prerequisites - **smina binary** — conda-forge or SourceForge build …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/smina-molecular-docking@sha256:d7ababdb48bcb6ddThe line at the top of this page pins the label git:20260528.0e69ced, 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_drz2cxgmyk4dgjoa)
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Versions
The registry has recorded 3 versions of this file, all committed on May 28, 2026.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260528.0e69ced latest | 2026-05-28 | 0e69ced | 14,751 B | A | view · diff |
| git:20260528.6b09274 | 2026-05-28 | 6b09274 | 14,779 B | A | view · diff |
| git:20260528.d3d04b2 | 2026-05-28 | d3d04b2 | 18,130 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 (14751 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_drz2cxgmyk4dgjoa GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/smina-molecular-docking GET https://markdownregistry.com/api/v1/blob/d7ababdb48bcb6dd230f91369e7ac5a469fca70354da3087c622500a876cb1a2
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.