molclaw-esmfold

name	molclaw-esmfold
description	Use ESMFold model to predict 3D structure of the input protein sequence.
license	MIT license
metadata	{"skill-author":"PJLab"}

Protein Structure Prediction

The description of tool pred_protein_structure_esmfold.

Use the ESMFold model for protein 3D structure prediction.
Args:
    sequence (str): Protein sequence
Return:
    status: success/error
    msg: message
    pdb_path (str): The predicted pdb file path

How to use tool pred_protein_structure_esmfold :

response = await client.session.call_tool(
    "pred_protein_structure_esmfold",
    arguments={
        "sequence": sequence
    }
)
result = client.parse_result(response)
pred_protein_structure = result["pdb_path"]

---

⚠ Mandatory Output File Download (L3 Principle 14)

After calling this tool, you MUST download all output structure files from the MCP server to the local workspace using server_file_to_base64. A tool call is NOT considered complete until its output files have been downloaded and verified locally (ls -la <file> — size must be > 0).

import base64, os
response = await client.session.call_tool(
    "server_file_to_base64",
    arguments={"file_path": result["output_file"]}  # or relevant output field
)
dl = client.parse_result(response)
local_path = "stepNN_descriptive_name.ext"
with open(local_path, "wb") as f:
    f.write(base64.b64decode(dl["base64_string"]))
assert os.path.getsize(local_path) > 0, f"Download failed: {local_path}"

Download policy: All structure output files are Category A (user-critical) — essential for user verification, downstream analysis, and reproducibility. When in doubt, download. Over-collection is always preferred over under-collection.

---

⚠ Confidence Metric Checkpoint (L3 Principle 12 Checkpoint A)

After ESMFold prediction, check pLDDT (stored in B-factor column):

• pLDDT > 85: Excellent confidence
• pLDDT 70-85: Good
• pLDDT < 70: Moderate to low — note in report as limitation
• pLDDT < 50: Very low — consider alternative structure sources

⚠ Numbering Scheme (L3 Principle 17)

ESMFold structures use 1-based sequential numbering from the input sequence. If the task references UniProt residue numbers, apply molclaw-residue-mapper to build the mapping before any residue-specific analysis.

⚠ Sequence Length Limitation

ESMFold quality degrades significantly for sequences > 800 residues. For longer proteins, use Chai-1 (molclaw-chai1-predict) instead.