biology
BioNeMo OpenFold2
BioNeMo OpenFold2NVIDIA NIM for OpenFold2 single-chain protein structure prediction.
Model details
View repositoryExample usage
Call BioNeMo OpenFold2 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/openfold2/predict-structure-from-msa-and-template"
9)
10
11sequence = "LSDEDFKAVFGMTRSAFANLPLWKQQNLKKEKGLF"
12minimal_msa_a3m = f">query\n{sequence}\n"
13
14payload = {
15 "sequence": sequence,
16 "input_id": "villin_hp35_test",
17 "selected_models": [1],
18 "alignments": {
19 "uniref90": {
20 "a3m": {
21 "alignment": minimal_msa_a3m,
22 "format": "a3m",
23 }
24 }
25 },
26 "use_templates": False,
27}
28
29response = requests.post(
30 BASETEN_URL,
31 headers={
32 "Authorization": f"Bearer {BASETEN_API_KEY}",
33 "Content-Type": "application/json",
34 },
35 json=payload,
36 timeout=300,
37)
38response.raise_for_status()
39result = response.json()
40print(result)
41JSON output
1{
2 "structures_in_ranked_order": [
3 {
4 "structure": "<PDB text>",
5 "format": "pdb"
6 }
7 ]
8}
