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Use P2Rank to locate binding pockets in the input protein. Unless specified by the user, prioritize using fpocket.
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| 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"} |
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"]
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.