# Proteinmpnn Nim

Run ProteinMPNN inverse folding via NVIDIA NIM to design protein sequences for a target...

- Repository: https://github.com/NVIDIA/skills (3812 stars)
- Category: Design
- License: Apache-2.0 AND CC-BY-4.0
- Last updated: 2026-10-30
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add NVIDIA/skills --skill proteinmpnn-nim -g -a claude-code -y`
Codex: `npx skills add NVIDIA/skills --skill proteinmpnn-nim -g -a codex -y`
Cursor: `npx skills add NVIDIA/skills --skill proteinmpnn-nim -g -a cursor -y`
Gemini CLI: `npx skills add NVIDIA/skills --skill proteinmpnn-nim -g -a gemini-cli -y`
Claude Code plugin marketplace: `/plugin marketplace add NVIDIA/skills`

## Description

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.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# 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. `NIM_API_MODE=local` selects
the local service at `PROTEINMPNN_NIM_URL`; 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 `PROTEINMPNN_NIM_URL`
  (default base URL: `http://localhost:8000`).

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.

## Data Transfer and Authorization

The rest: https://github.com/NVIDIA/skills/blob/HEAD/skills/bionemo-proteinmpnn-nim/SKILL.md