molclaw-p2rank

What problem does it solve?

The skill automates detection of ligand binding pockets from protein structure files to produce reliable pocket coordinates and confidence scores for docking and virtual screening, reducing manual inspection and inconsistent pocket selection.

Core Features & Use Cases

• P2Rank-based pocket prediction: Execute P2Rank to predict and rank ligand binding pockets by confidence.
• fpocket prioritization and compatibility: Integrate fpocket as a prioritized alternative when not explicitly overridden by the user.
• Docking box enforcement: Enforce a minimum docking box size of 25.0 Å per axis to ensure robust downstream docking.
• Use Case: Given a PDB file for a target protein, identify the top-ranked pocket center and prepare standardized box coordinates for molecular docking or virtual screening.

Quick Start

Predict binding pockets for the protein file my_protein.pdb and return the top-ranked pocket coordinates, site identifiers, and confidence scores.