molclaw-fpocket-toolkit-base

What problem does it solve?

This Skill automates detection of ligand binding pockets from protein structure files and returns parsed pocket descriptors and preserved run artifacts for downstream analysis and docking preparation.

Core Features & Use Cases

• Pocket Detection: Runs fpocket_toolkit on PDB/mmCIF inputs and parses pocket descriptors including scores, centers, and sizes.
• Filtering & Export: Supports top-N selection, druggability threshold filtering, verbose parsing, and returns output files plus an organized run directory.
• Docking Safety Rule: Enforces a minimum 25.0 Å per dimension when converting pocket dimensions to docking box sizes to ensure reliable docking inputs.
• Use Case: Prepare standardized pocket descriptors and docking boxes for virtual screening, hit identification, and structure-based optimization workflows.

Quick Start

Use the molclaw-fpocket-toolkit-base skill to analyze the uploaded PDB file and return parsed pocket descriptors, run artifacts, and output file paths.