Agent skill · nvidia
proteinmpnn-nim
Run ProteinMPNN inverse folding via NVIDIA NIM to design protein sequences for a target backbone. Sends user-provided PDB files and design parameters to NVIDIA's hosted API, authenticated with an environment API key, or to a user-selected local NIM. Use for sequence design, backbone redesign, fixed chains and residues, omit_AAs, sampling temperature, soluble model, local Docker, and multi-FASTA output.
What it needs
About 4k tokens when loaded.
What this skill does
ProteinMPNN NIM <!-- nv-carps: dummy edit to trigger NIM skill validation. --> Design protein sequences for a supplied backbone PDB. 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: inverse-folding uses, limits, and validation. references/parameters.md: design controls, fixed positions, sampling. references/validation.md: FASTA, score, and structure checks. references/examples.md: compact hosted/local request patterns. Choose Mode Honor the user's explicit mode; otherwise use the configured runtime. NIMAPIMODE=local selects the local service at PROTEINMPNNNIMURL; the URL defaults to http://localhost:8000 for a NIM running in the same host or container. Ask only when neither the environment nor the user's request makes the mode clear: Hosted NVIDIA API or local Docker NIM? Hosted: https://health.api.nvidia.com/v1/biology/ipd/proteinmpnn/predict Local: append /biology/ipd/proteinmpnn/predict to PROTEINMPNNNIMURL (default base URL: http://localhost:8000). 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. Data Transfer and Authorization Before a hosted request, tell the user that the entire PDB file and design parameters will be uploaded to NVIDIA's hosted API at the endpoint above. Proceed if the user has explicitly requested hosted processing of that PDB or already approved the transfer; otherwise ask for confirmation before submitting. For confidential structures, recommend a local NIM in the user's approved environment. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills nvidia/bionemo-proteinmpnn-nim