proteinmpnn-nim

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Run ProteinMPNN inverse folding via NVIDIA NIM to design protein sequences for a target backbone. Use for ProteinMPNN, inverse folding, sequence design, backbone redesign, fixed chains/residues, omit_AAs, sampling temperature, soluble model, hosted NVIDIA API, local Docker, PDB input, and multi-FASTA output.

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Sourcenvidia-bionemo/bionemo-agent-toolkit

Added on2026-08-21

NPX Install

npx skill4agent add nvidia-bionemo/bionemo-agent-toolkit proteinmpnn-nim

SKILL.md Content

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ProteinMPNN NIM

Design protein sequences for a supplied backbone PDB. Use this

SKILL.md

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 an explicitly configured runtime before asking.

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:

${PROTEINMPNN_NIM_URL:-http://localhost:8000}/biology/ipd/proteinmpnn/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.

Local Docker

For local setup, run the full sequence — env preflight,

docker login

,

docker run

, readiness loop, then the no-auth localhost request; do not answer with only a localhost Python request. For the exact preflight (

.env

sourcing,

NGC_API_KEY

/

NVIDIA_API_KEY

handling, and the

docker run

for

nvcr.io/nim/ipd/proteinmpnn:latest

), copy the command block in

references/api.md

under Docker Reference verbatim. This NIM's cache mount is

/home/nvs/.cache/nim

, not

/opt/nim/.cache

. When

PROTEINMPNN_NIM_URL

is supplied, the service is already managed elsewhere; use that URL and do not start another Docker container.

Readiness:

bash

proteinmpnn_nim_url="${PROTEINMPNN_NIM_URL:-http://localhost:8000}"
until curl -sf "${proteinmpnn_nim_url%/}/v1/health/ready"; do sleep 5; done

Request Pattern

Read PDB content inline; do not send only a file path.

python

import os
from pathlib import Path
import requests

HOSTED = os.getenv("NIM_API_MODE", "hosted").strip().lower() != "local"
pdb_content = Path("1R42.pdb").read_text()
nim_url = os.getenv("PROTEINMPNN_NIM_URL", "http://localhost:8000").rstrip("/")
url = (
    "https://health.api.nvidia.com/v1/biology/ipd/proteinmpnn/predict"
    if HOSTED else f"{nim_url}/biology/ipd/proteinmpnn/predict"
)
headers = {"Content-Type": "application/json"}
if HOSTED:
    headers["Authorization"] = f"Bearer {os.environ['NGC_API_KEY']}"

payload = {
    "input_pdb": pdb_content,
    "num_seq_per_target": 10,
    "sampling_temp": [0.1],
    "use_soluble_model": False,
    "ca_only": False,
}
response = requests.post(url, headers=headers, json=payload, timeout=300)
response.raise_for_status()
result = response.json()

Common controls:

Redesign only chain A:
```
"input_pdb_chains": ["A"]
```
.
Exclude amino acids:
```
"omit_AAs": ["C"]
```
or
```
"omit_AAs": ["M"]
```
.
Diversity:
```
"sampling_temp": [0.1, 0.3, 0.5]
```
(always a list).
Solubility bias:
```
"use_soluble_model": True
```
.
Candidate count:
```
num_seq_per_target
```
is 1-100.

Save And Report Output

Save the returned

mfasta

and pair scores only with designed (non-native/WT) rows, using the snippet in

references/examples.md

under Save Multi-FASTA. Validate promising designs by predicting structures with Boltz2 or OpenFold3 and comparing them to the target backbone. For FASTA/score sanity checks, read

references/validation.md

.

Limits And Troubleshooting

Minimum GPU VRAM: about 3 GB.
```
sampling_temp
```
must be a list, even for one value.
Empty
```
mfasta
```
: check non-empty
```
input_pdb
```
and
```
num_seq_per_target >= 1
```
.
PDB parse errors: use valid PDB ATOM records.
Local URL 404 usually means an accidental
```
/v1/
```
prefix.
Cache mount error: use
```
/home/nvs/.cache/nim
```
inside the container.