molclaw-p2rank

name	molclaw-p2rank
description	Use P2Rank to locate binding pockets in the input protein. Unless specified by the user, prioritize using fpocket.
license	MIT license
metadata	{"skill-author":"PJLab"}

Pocket Location

The description of tool pred_pocket_prank.

Use P2Rank to predict ligand binding pockets in the input protein.
Args:
    pdb_file_path (str): Path to the protein structure file (PDB format)
Return:
    status (str): success/error
    msg (str): message
    pred_pockets (List[dict]): List of dict, each containing pocket confidence and center position information. The first pocket (pred_pockets[0]) has the highest score and is usually used for molecular docking.
        --site_id (str): Pocket id
        --probability (float): Predicted confidence score (0~1) of the pocket
        --center_x (float): Center X of the pocket
        --center_y (float): Center Y of the pocket 
        --center_z (float): Center Z of the pocket

How to use tool pred_pocket_prank :

response = await client.session.call_tool(
    "pred_pocket_prank",
    arguments={
        "pdb_file_path": pdb_file_path
    }
)
result = client.parse_result(response)
pred_pockets = result["pred_pockets"]

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⚠ Docking Box Size Enforcement (L3 Principle 18)

When P2Rank pocket dimensions are used for downstream docking, enforce a minimum of 25.0 Å per dimension. If any dimension is less than 25 Å, override to 25.0 Å.