msa-structure-prediction-pipeline

Files (5)

• BENCHMARK.md
• SKILL.md
• evals.json · evals/
• skill-card.md
• skill.oms.sig

SKILL.md (first lines)

# MSA Structure Prediction Pipeline

Predict protein structures with high accuracy by chaining two BioNeMo NIMs:

```
Step 1: MSA-Search  →  Step 2: OpenFold3
(Search homologs)       (Predict structure with MSA)
```

---

## Overview

Why chain these NIMs?
- **MSA-Search** finds evolutionary homologs in UniRef30 and ColabFold databases using GPU-accelerated MMSeqs2. The resulting alignment provides crucial evolutionary information.
- **OpenFold3** uses the MSA to improve structure prediction accuracy — especially for sequences where no close homolog exists in PDB.
- Running MSA-Search first means OpenFold3 gets the full evolutionary context rather than a single-sequence prediction.

---

## Before you start

Confirm with the user:
1. **Query sequence**: amino acid sequence to predict
2. **MSA depth**: how many sequences to retrieve (default 500; more = slower but more context)
3. **API mode**: hosted or local Docker?

Note: local MSA-Search requires 1.4 TB of database storage — strongly recommend hosted unless the user has that infrastructure.

For local Docker, do not assume MSA-Search and OpenFold3 are both on
`localhost:8000` concurrently. Run one container at a time and hand off the A3M
file, or start each NIM on a distinct host port and set the URLs explicitly.

---

## Step 1: Search for MSA with MSA-Search

```python
import requests, json, os
from pathlib import Path

NGC_API_KEY = os.getenv("NGC_API_KEY")
HOSTED = True

query_sequence = "<YOUR_PROTEIN_SEQUENCE>"

if HOSTED:
    msa_url = "https://health.api.nvidia.com/v1/biology/colabfold/msa-search/predict"
    headers = {"Content-Type": "application/json",
               "Authorization": f"Bearer {NGC_API_KEY}"}
else:
    msa_url = "http://localhost:8000/biology/colabfold/msa-search/predict"
    headers = {"Content-Type": "application/json"}

payload = {
    "sequence": query_sequence,
    "databases": ["Uniref30_2302", "colabfold_envdb_202108"],
    "e_value": 0.0001,
    "output_alignment_formats": ["a3m"],
}

r = requests.post(msa_url, headers=headers, json=payload)
r.raise_for_status()
msa_result = r.json()

# Extract the A3M alignment
a3m_alignment = msa_result["alignments"]["Uniref30_2302"]["a3m"]["alignment"]

# Save for reference
with open("query_msa.a3m", "w") as f:
    f.write(a3m_alignment)

# Count sequences in alignment
n_seqs = a3m_alignment.count(">")
print(f"Step 1 complete: found {n_seqs} homologous sequences")
print(f"MSA saved to query_msa.a3m")
```

---

## Step 2: Predict structure with OpenFold3

Pass the MSA directly into OpenFold3's `msa` field:

```python
if HOSTED:
    of3_url = "https://health.api.nvidia.com/v1/biology/openfold/openfold3/predict"
else:
    of3_url = "http://localhost:8000/biology/openfold/openfold3/predict"

# Build the OpenFold3 MSA structure from the retrieved alignment
msa_data = {
    "uniref30": {
        "a3m": {
            "alignment": a3m_alignment,
            "format": "a3m"
        }
    }
}

# Optionally also include colabfold_envdb alignment if requested
# env_alignment = msa_result["alignments"]["colabfold_envdb"]["a3m"]["alignment"]
# msa_data["colabfold_env"] = {"a3m": {"alignment": env_alignment, "format": "a3m"}}

payload = {
    "inputs": [{
        "input_id": "prediction_with_msa",
        "output_format": "pdb",
        "molecules": [
            {
                "type": "protein",
                "sequence": query_sequence,
                "diffusion_samples": 1,
                "msa": msa_data
            }
        ]
    }]
}

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