BioNeMo OpenFold3

NVIDIA NIM for OpenFold3 diffusion-based structure prediction.

Deploy now

Model details

Developed by
NVIDIA
Model family
BioNeMo
Use case
biology
Variant
NIM
Hardware
H100
License
NVIDIA AI Foundation Models Community License Agreement

View repository

Example usage

Call BioNeMo OpenFold3 on Baseten using the NIM structure prediction route.

Note: You need to procure your own NVAIE licenses to access this NIM.

Input

1import os
2import requests
3
4MODEL_ID = os.environ["BASETEN_MODEL_ID"]
5BASETEN_API_KEY = os.environ["BASETEN_API_KEY"]
6BASETEN_URL = (
7    f"https://model-{MODEL_ID}.api.baseten.co/environments/production/sync"
8    "/biology/openfold/openfold3/predict"
9)
10
11sequence = "LSDEDFKAVFGMTRSAFANLPLWKQQNLKKEKGLF"
12minimal_msa = f">query\n{sequence}\n"
13
14payload = {
15    "inputs": [
16        {
17            "input_id": "villin_hp35_test",
18            "molecules": [
19                {
20                    "type": "protein",
21                    "sequence": sequence,
22                    "msa": {
23                        "main": {
24                            "a3m": {
25                                "alignment": minimal_msa,
26                                "format": "a3m",
27                            }
28                        }
29                    },
30                }
31            ],
32            "diffusion_samples": 1,
33            "output_format": "pdb",
34        }
35    ]
36}
37
38response = requests.post(
39    BASETEN_URL,
40    headers={
41        "Authorization": f"Bearer {BASETEN_API_KEY}",
42        "Content-Type": "application/json",
43    },
44    json=payload,
45    timeout=300,
46)
47response.raise_for_status()
48result = response.json()
49print(result)
50

JSON output

1{
2    "outputs": [
3        {
4            "input_id": "villin_hp35_test",
5            "structures_with_scores": [
6                {
7                    "structure": "<PDB text>",
8                    "format": "pdb",
9                    "confidence_score": 0.85
10                }
11            ]
12        }
13    ]
14}