Protein Preparation

Protein preparation converts a raw, as-deposited PDB structure into a chemically and geometrically valid model suitable for docking calculations, correcting...

Protein preparation converts a raw, as-deposited PDB structure into a chemically and geometrically valid model suitable for docking calculations, correcting the numerous artefacts and omissions inherent to experimental structure determination. This preparation process removes crystallographic water molecules (except where a specific structural water is known to mediate ligand binding and is therefore deliberately retained), adds hydrogen atoms that are not resolved by X-ray diffraction, assigns appropriate protonation states to ionisable residues at physiological pH, resolves side-chain and loop conformational ambiguities, and performs a restrained energy minimisation to relieve unfavourable steric clashes introduced during hydrogen addition, all without significantly perturbing the experimentally determined heavy-atom backbone conformation.