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Protein Fold

Protein structure prediction using ESMFold (Meta) and OpenFold3 (NVIDIA). Paste an amino acid sequence to get a 3D PDB structure with interactive 3Dmol viewer. Two backends: ESMFold via the ESM Atlas API for single-chain folding, and OpenFold3 via NVIDIA Health API for protein-DNA complex prediction.

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Overview

The Protein Fold app provides two structure prediction backends. ESMFold takes a single amino acid sequence (10–400 residues) and returns a PDB structure via Meta's ESM Atlas API. OpenFold3 takes a protein sequence plus two DNA sequences and predicts the protein-DNA complex via NVIDIA's Health API. The web UI includes an interactive 3Dmol viewer with cartoon/sphere/stick/line rendering, spin control, and PDB download.

Data Source

ESMFold — api.esmatlas.com/foldSequence/v1/pdb/ (Meta AI). OpenFold3 — health.api.nvidia.com (NVIDIA BioNeMo).

Endpoints

POST /protein_fold/predict — Fold sequence (web UI, JSON)

Predict 3D structure from amino acid sequence. Returns PDB content, atom count, residue count, amino acid composition, and molecular weight.

curl -X POST "https://atomgpt.org/protein_fold/predict" \
  -H "Authorization: Bearer sk-XYZ" \
  -H "Content-Type: application/json" \
  -H "accept: application/json" \
  -d '{
    "sequence": "MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGDGTQDNLSGAEKAVQVKVKALPDAQFEVVHSLAKWKRQQQ"
  }'
Field Type Description
sequence string Amino acid sequence (standard one-letter codes: ACDEFGHIKLMNPQRSTVWY, 10–400 residues)

Response:

Field Description
pdb_content Full PDB file content
sequence Cleaned uppercase sequence
sequence_length Number of residues
num_atoms Total atoms in PDB
num_residues Unique residue count
composition Amino acid composition dict (e.g. {"ALA": 5, "GLY": 3})
molecular_weight Estimated molecular weight (Da)

GET /protein_fold/query — Fold sequence (API key, plain text PDB)

Returns the raw PDB file as plain text.

curl "https://atomgpt.org/protein_fold/query?sequence=MKTAYIAKQRQISFVKSHFS&APIKEY=sk-XYZ" \
  -H "accept: text/plain" \
  --output structure.pdb

POST /protein_fold/query — Fold sequence (session auth, ZIP or JSON)

Returns PDB as a ZIP file (default) or JSON.

curl -X POST "https://atomgpt.org/protein_fold/query" \
  -H "Authorization: Bearer sk-XYZ" \
  -H "Content-Type: application/x-www-form-urlencoded" \
  -d "sequence=MKTAYIAKQRQISFVKSHFS&format=zip" \
  --output protein_structure.zip
Param Default Description
sequence required Amino acid sequence
format "zip" "zip" (PDB in ZIP archive) or "json" (PDB as JSON string)

GET /openfold/query — Protein-DNA complex (NVIDIA OpenFold3)

Predict a protein-DNA complex structure using NVIDIA's OpenFold3 API.

curl "https://atomgpt.org/openfold/query?protein_sequence=MKTAYIAKQRQISFVKSHFS&dna1=ATCGATCG&dna2=CGATCGAT&APIKEY=sk-XYZ" \
  -H "accept: text/plain" \
  --output complex.pdb
Param Description
protein_sequence Protein amino acid sequence
dna1 First DNA strand sequence
dna2 Second DNA strand sequence (complementary)

Returns plain-text PDB of the predicted complex.

Python Examples

import requests

response = requests.post(
    "https://atomgpt.org/protein_fold/predict",
    headers={
        "Authorization": "Bearer sk-XYZ",
        "accept": "application/json",
        "Content-Type": "application/json",
    },
    json={
        "sequence": "KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL"
    },
)
data = response.json()
if data["success"]:
    print(f"Residues: {data['num_residues']}")
    print(f"Atoms: {data['num_atoms']}")
    print(f"MW: {data['molecular_weight']:.0f} Da")
    with open("structure.pdb", "w") as f:
        f.write(data["pdb_content"])
    print("Saved structure.pdb")

import requests

response = requests.get(
    "https://atomgpt.org/protein_fold/query",
    params={
        "sequence": "MKTAYIAKQRQISFVKSHFS",
        "APIKEY": "sk-XYZ",
    },
)
with open("peptide.pdb", "w") as f:
    f.write(response.text)

import requests

response = requests.get(
    "https://atomgpt.org/openfold/query",
    params={
        "protein_sequence": "MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGD",
        "dna1": "ATCGATCGATCG",
        "dna2": "CGATCGATCGAT",
        "APIKEY": "sk-XYZ",
    },
)
with open("complex.pdb", "w") as f:
    f.write(response.text)
print("Saved protein-DNA complex PDB")

AGAPI Agent

from agapi.agents import AGAPIAgent
import os

agent = AGAPIAgent(api_key=os.environ.get("AGAPI_KEY"))

# Fold protein
response = agent.query_sync("Fold this protein sequence: MKTAYIAKQRQISFVKSHFS")
print(response)

References