drug-pose-validation

Goal

To filter docked or generated ligand poses through physical plausibility checks (bond lengths, angles, planarity, internal clashes, protein-ligand clashes, stereochemistry) using PoseBusters, producing a validated subset of poses plus a machine-readable report.

This skill sits between docking (drug-docking-vina) and downstream refinement (drug-complex-system-builder, drug-protein-ligand-md), ensuring that only physically reasonable poses enter expensive simulation stages.

Instructions

1. Prepare inputs

You need:

• Docked poses: an SDF file containing one or more ligand poses (e.g., output from Vina converted to SDF, or from any pose-generation tool).
• Receptor structure (optional but recommended): PDB file of the protein. When provided, PoseBusters also checks for protein-ligand steric clashes.

If your docked poses are in PDBQT format, convert them to SDF first: