Msa Search Nim
Generate multiple sequence alignments (MSAs) for protein sequences using the ColabFold...
Install
npx skills add NVIDIA/skills --skill msa-search-nim -g -a claude-code -y- Repository
- NVIDIA/skills3.8k
- Category
- DevOps
- Updated
- 5d ago
- License
- Apache-2.0 AND CC-BY-4.0
- Context cost
- Mediumabout 3,000 tokens
- Runs scripts
- Yes, review before use
What it does
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 docker run uses the slow built-in downloader.
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
Local inference paths do not include /v1/. Hosted requests use Authorization: Bearer $NGC_API_KEY. Supported local Docker
startup uses NGC_API_KEY (or NVIDIA_API_KEY via the preflight) for
registry login, entitlement checks, and first-run model downloads; pass it
into the container with -e NGC_API_KEY. Local inference requests use no
auth header after readiness. Warm-cache key-free startup varies by
image/version and should not be assumed.
The hosted template path returned HTTP 404 in validation, so use local Docker
for template search unless the hosted docs/service changes.
