drug-redocking-rmsd

Goal

To quantitatively validate a docking protocol by computing the symmetry-corrected in-place heavy-atom RMSD between docked poses and the crystallographic reference ligand. A top-scored pose (pose 1) RMSD below 2.0 A is the standard threshold for a successful self-docking control.

Self-docking is a necessary, not sufficient, check. It verifies that your receptor preparation, box definition, and scoring function can recover a known pose in its own binding site. It does not verify that the protocol will work on new compounds. For a production virtual screen, complement self-docking with cross-docking into different receptor conformations when available (see the HTVS workflow Stage 3), and pair this RMSD check with drug-pose-validation to catch poses that are geometrically near-native but physically implausible (internal clashes, strained torsions).

Instructions

1. Compute RMSD from a crystal PDB reference

When the reference ligand is extracted from a PDB (HETATM records, no bond orders), provide the SMILES so the script can assign bond orders via template matching: