drug-redocking-rmsd

What problem does it solve?

This Skill determines whether an AI docking protocol can reliably reproduce a crystallographic ligand pose by computing symmetry-corrected heavy-atom RMSD between docked poses and a reference ligand.

Core Features & Use Cases

• Symmetry-corrected in-place heavy-atom RMSD: Computes the minimum heavy-atom RMSD over molecular automorphisms without rigid-body alignment to ensure docking-valid “in-place” validation.
• Top-poses protocol gate: Produces a pass/fail verdict based on whether the top-scored pose (pose 1) falls below a configurable RMSD threshold.
• Ligand identity safety check: Verifies reference and docked compounds match via InChIKey connectivity so the result cannot silently compare unrelated molecules.
• Handles common reference formats: Accepts reference ligands as PDB (requires SMILES for bond-order assignment) or SDF (bond orders included).

Quick Start

Compute the RMSD gate by running the Skill’s compute_rmsd.py on your Vina multi-model PDBQT and a crystal reference ligand file, supplying SMILES if the reference is a PDB.