msa-search-nim SKILL.md skillA
This file is byte-identical to the first copy the registry indexed, one of 3 indexed copies. Same content hash, so the same checks give both the same grade.
msa-search-nim from nvidia-bionemo/bionemo-agent-toolkit is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add nvidia-bionemo/bionemo-agent-toolkit/msa-search-nim@git:20260930.58a950aPins git:20260930.58a950a in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- nvidia-bionemo/bionemo-agent-toolkit
- Path
nim-skills/msa-search-nim/SKILL.md- Versions recorded
- 4
- Latest version
- git:20260930.58a950a, committed Sep 30, 2026
- First version recorded
- Jun 23, 2026
- Size
- 18,248 bytes
- Repository stars
- 503
- License
- a license file GitHub does not identify
Generate multiple sequence alignments (MSAs) for protein sequences using the ColabFold MSA-Search NIM. Use for homolog search, UniRef30/ColabFold env searches, A3M or FASTA alignments, paired MSA search for complexes, PDB70 structural templates, hosted NVIDIA API calls, or local Docker deployment. For local deployment, download the databases in parallel with aria2c and launch via NIM_MODEL_NAME (the recommended default fast path, ~14 min vs over 80 min for the built-in downloader); a plain…
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
# MSA-Search NIM Generate protein MSAs with GPU-accelerated MMSeqs2. Use this guide for first-pass hosted/local usage; load supplemental files only when needed: - `references/api.md`: exact endpoints, schemas, Docker flags, response fields. - `references/science.md`: MSA purpose, pairing/templates, limits, handoffs. - `references/parameters.md`: database, pairing, depth, and template tuning. - `references/validation.md`: alignment, template, and artifact checks. - `references/examples.md`: compact hosted/local request patterns. ## Choose Mode And Endpoint Ask only when context is unclear: > Hosted NVIDIA API or local Docker NIM? - Hosted standard MSA: `https://health.api.nvidia.com/v1/biology/colabfold/msa-search/predict` - Hosted paired MSA: `https://health.api.nvidia.com/v1/biology/colabfold/msa-search/paired/predict` - Local standard MSA: `http://localhost:8000/biology/colabfold/msa-search/predict` - Local paired MSA: `http://localhost:8000/biology/colabfold/msa-search/paired/predict` - Local templates: `http://localhost:8000/biology/colabfold/msa-search/structure-templates/predict` …
Read the whole file at its exact version.
How to install
mdr add nvidia-bionemo/bionemo-agent-toolkit/msa-search-nim@sha256:3d42c5136c5da1bcThe line at the top of this page pins the label git:20260930.58a950a, 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_g6puxeyd3uxq3bak)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 4 versions of this file, between Jun 23, 2026 and Sep 30, 2026, about one every 33 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260930.58a950a latest | 2026-09-30 | 58a950a | 18,248 B | A | view · diff |
| git:20260812.47315cc | 2026-08-12 | 47315cc | 16,808 B | A | view · diff |
| git:20260723.8f328ad | 2026-07-23 | 8f328ad | 16,744 B | A | view · diff |
| git:20260623.4e8fda7 | 2026-06-23 | 4e8fda7 | 6,511 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 (18248 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
nvidia-bionemo/bionemo-agent-toolkit · 503 stars · license a license file GitHub does not identify · pushed 2026-11-05 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_g6puxeyd3uxq3bak GET https://markdownregistry.com/api/v1/resolve?ref=nvidia-bionemo/bionemo-agent-toolkit/msa-search-nim GET https://markdownregistry.com/api/v1/blob/3d42c5136c5da1bce8862e67fea25740958c7daba1f27a1c612695ac4dd03062
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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