Agent skill · nvidia
msa-search-nim
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.
What it needs
About 9k tokens when loaded.
What this skill does
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 $NGCAPIKEY. Supported local Docker startup uses NGCAPIKEY (or NVIDIAAPIKEY via the preflight) for registry login, entitlement checks, and first-run model downloads; pass it into the container with -e NGCAPIKEY. 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. Local Docker Default local deployment = parallel download + NIMMODELNAME. The first recipe below is the one to use for real workflows. It downloads the database(s) with a range-parallel downloader (aria2c) and starts the NIM against those files — ~14 min for UniRef30 vs >80 min for the NIM's built-in downloader (measured, H100). …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills nvidia/bionemo-msa-search-nim