rfdiffusion-nim

Original：🇺🇸 English

Translated

Run RFDiffusion protein backbone design via NVIDIA NIM. Use for de novo protein backbones, motif scaffolding, binder design, hotspot residues, contigs syntax, diffusion steps, hosted NVIDIA API calls, local Docker deployment, and PDB backbone outputs for ProteinMPNN sequence design.

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Sourcenvidia-bionemo/bionemo-agent-toolkit

Added on2026-08-21

NPX Install

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

SKILL.md Content

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RFDiffusion NIM

Design protein backbone PDBs for de novo proteins, motif scaffolds, and binders. 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
```
: design modes, strengths, limits, and handoffs.
```
references/parameters.md
```
: contigs, hotspots, steps, and seeds.
```
references/validation.md
```
: PDB, contig, and artifact sanity checks.
```
references/examples.md
```
: compact hosted/local request patterns.

Choose Mode

Ask only when context is unclear:

Hosted NVIDIA API or local Docker NIM?

Hosted:

https://health.api.nvidia.com/v1/biology/ipd/rfdiffusion/generate

Local:

http://localhost:8000/biology/ipd/rfdiffusion/generate

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 answers, copy the preflight below exactly before

docker login

,

docker run

, readiness, and the no-auth local request. Do not replace it with a simple

: "${NGC_API_KEY:?Set NGC_API_KEY}"

check, do not invent a cache default, and do not drop the

NVIDIA_API_KEY

fallback. Default setup is single GPU

device=0

.

bash

set -a
[ -f .env ] && . ./.env
set +a

if [ -z "${NGC_API_KEY:-}" ] && [ -n "${NVIDIA_API_KEY:-}" ]; then
  export NGC_API_KEY="$NVIDIA_API_KEY"
fi
: "${NGC_API_KEY:?Set NGC_API_KEY or NVIDIA_API_KEY}"
: "${LOCAL_NIM_CACHE:?Set LOCAL_NIM_CACHE}"

echo "$NGC_API_KEY" | docker login nvcr.io --username '$oauthtoken' --password-stdin

mkdir -p "${LOCAL_NIM_CACHE}"
chmod 755 "${LOCAL_NIM_CACHE}"

docker run -it \
  --runtime=nvidia \
  --gpus "device=0" \
  -e NGC_API_KEY \
  -v "${LOCAL_NIM_CACHE}:/opt/nim/.cache" \
  -p 8000:8000 \
  nvcr.io/nim/ipd/rfdiffusion:2

Readiness:

bash

until curl -sf http://localhost:8000/v1/health/ready; do sleep 5; done

Contigs DSL

contigs

defines what to keep and what to generate. For the full pattern syntax (fixed length, ranges, kept chain segments, chain breaks), see

references/api.md

under Contigs Language Reference.

Design modes:

De novo:
```
contigs="80-120"
```
; live hosted validation requires a non-empty
```
input_pdb
```
or
```
input_pdb_asset
```
, so inline requests should include the dummy PDB below.
Motif scaffolding: read
```
target.pdb
```
, pass
```
input_pdb
```
, use a contig like
```
"A25-35/0 50-80"
```
.
Binder design: pass target
```
input_pdb
```
, contig with target and binder segment, and
```
hotspot_res=["A50", "A51", ...]
```
in ChainResidue string format.

python

DUMMY_PDB = (
    "CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 1           1\n"
    "ATOM      1  CA  ALA A   1       0.000   0.000   0.000  1.00  0.00           C\n"
    "END\n"
)

Request Pattern

python

import os
from pathlib import Path
import requests

HOSTED = True
url = (
    "https://health.api.nvidia.com/v1/biology/ipd/rfdiffusion/generate"
    if HOSTED else "http://localhost:8000/biology/ipd/rfdiffusion/generate"
)
headers = {"Content-Type": "application/json"}
if HOSTED:
    headers["Authorization"] = f"Bearer {os.getenv('NGC_API_KEY')}"

payload = {
    "input_pdb": DUMMY_PDB,
    "contigs": "80-120",
    "diffusion_steps": 50,
}
response = requests.post(url, headers=headers, json=payload, timeout=300)
response.raise_for_status()
result = response.json()
Path("designed_backbone.pdb").write_text(result["output_pdb"])

Motif scaffold:

python

payload = {
    "input_pdb": Path("target.pdb").read_text(),
    "contigs": "A25-35/0 50-80",
    "diffusion_steps": 50,
}

Binder design:

python

payload = {
    "input_pdb": Path("target.pdb").read_text(),
    "contigs": "A1-100/0 50-100",
    "hotspot_res": ["A50", "A51", "A52", "A53", "A54"],
    "diffusion_steps": 50,
}

Save And Interpret Output

Save

result["output_pdb"]

as a PDB artifact and report

elapsed_ms

when present. Generated backbones are not final proteins; feed them to ProteinMPNN for sequence design, then validate sequences/structures with Boltz2 or OpenFold3. For PDB and contig checks, read

references/validation.md

.

Limits And Troubleshooting

```
diffusion_steps
```
: 1-50; 50 is maximum quality, fewer is faster.
Single GPU; minimum GPU VRAM is about 12 GB.
```
hotspot_res
```
uses strings like
```
"A50"
```
, not tuples.
```
422
```
usually means chain IDs in
```
contigs
```
/
```
hotspot_res
```
do not match
```
input_pdb
```
, a malformed contig, or omitted
```
input_pdb
```
for hosted de novo.
Local URL 404 usually means an accidental
```
/v1/
```
prefix.

rfdiffusion-nim

NPX Install

Tags

SKILL.md Content

RFDiffusion NIM

Choose Mode

Local Docker

Contigs DSL

Request Pattern

Save And Interpret Output

Limits And Troubleshooting