molclaw-protein-structure-retrieve

name	molclaw-protein-structure-retrieve
description	Retrieve and download protein structure file (pdb format) using gene name, Uniprot ID or PDB ID.
license	MIT license
metadata	{"skill-author":"PJLab"}

Retrieve Protein Structure

Scene 1: If the gene name is provided, please use tool retrieve_protein_structure_by_gene_name.

The description of tool retrieve_protein_structure_by_gene_name.

Retrieve and download the protein structure (.pdb) file using standard gene name.
Args:
    gene_name (str): Input gene name (e.g., 'TP53')
    organism (str): Species NCBI Taxonomy ID (default: 9606 for human, 10090 for mouse)
    sort_by (str): The sorting strategy defaults ('length') to prioritizing sequence length for maximum coverage, with an alternative option ('resolution') to prioritize structural resolution. 
Return:
    status (str): success/error
    msg (str): message
    prot_structure_path (str): Path to the downloaded protein structure file (pdb format)

How to use tool retrieve_protein_structure_by_gene_name :

response = await client.session.call_tool(
    "retrieve_protein_structure_by_gene_name",
    arguments={
        "gene_name": gene_name,
        "organism": "9606",
        "sort_by": "length"
    }
)
result = client.parse_result(response)
prot_structure_path = result["prot_structure_path"]

Scene 2: If the UniProt ID is provided, please use tool retrieve_protein_structure_by_uniprot_id.

The description of tool retrieve_protein_structure_by_uniprot_id.

Retrieve and download the protein structure (.pdb) file using uniprot id.
Args:
    uniprot_id (str): Input uniprot id (e.g., 'P04637')
    sort_by (str): The sorting strategy defaults ('length') to prioritizing sequence length for maximum coverage, with an alternative option ('resolution') to prioritize structural resolution. 
Return:
    status (str): success/error
    msg (str): message
    prot_structure_path (str): Path to the downloaded protein structure file (pdb format)

How to use tool retrieve_protein_structure_by_uniprot_id :

response = await client.session.call_tool(
    "retrieve_protein_structure_by_uniprot_id",
    arguments={
        "uniprot_id": uniprot_id,
        "sort_by": "length"
    }
)
result = client.parse_result(response)
prot_structure_path = result["prot_structure_path"]

Scene 3: If the PDB ID is provided, please use tool retrieve_protein_structure_by_pdb_id.

The description of tool retrieve_protein_structure_by_pdb_id.

Retrieve and download the protein structure (.pdb) file using pdb id.
Args:
    pdb_id (str): Input pdb id (e.g., "2l3r", "5XYF")
Return:
    status (str): success/error
    msg (str): message
    prot_structure_path (str): Path to the downloaded protein structure file (pdb format)

How to use tool retrieve_protein_structure_by_pdb_id :

response = await client.session.call_tool(
    "retrieve_protein_structure_by_uniprot_id",
    arguments={
        "pdb_id": pdb_id
    }
)
result = client.parse_result(response)
prot_structure_path = result["prot_structure_path"]

---

⚠ Mandatory Structure File Download (L3 Principle 14)

After retrieving a protein structure, download the PDB file from the MCP server to the local workspace. This is a Category A file — the foundation for all downstream workflows. Also download the FASTA file if provided.

⚠ Record Numbering Scheme (L3 Principle 17)

After downloading, document the structure's residue numbering scheme in run_log.md:

• RCSB PDB: check DBREF records for UniProt offset
• AlphaFold: uses UniProt canonical numbering
• If the task references specific residues, plan a mapping step using molclaw-residue-mapper