molclaw-equiscore-docking

What problem does it solve?

This Skill automates the multi-step process of ranking candidate molecules by docking score against a target protein, reducing manual orchestration across receptor preparation, pose generation, and scoring.

Core Features & Use Cases

• Receptor Preparation & Chain Extraction: Retrieve or accept a PDB, optionally extract chains, and fix structures with PDBFixer for robust docking.
• Pose Generation and Format Conversion: Convert SMILES to appropriate docked SDF poses when needed and map ligand identifiers to SMILES for reliable traceability.
• EquiScore Pocket Extraction and Screening: Run EquiScore pocket extraction and batch screening, then rank and return predictions while enforcing mandatory local download of all output structure files for verification and reproducibility.

Quick Start

Use molclaw-equiscore-docking to rank a list of candidate SMILES against a provided PDB and return the top-scoring molecules with downloaded output files.