GOLD allows for partial protein flexibility in all dockings. Specifically GOLD rotates the torsion angles of serine, threonine and tyrosine hydroxyl groups during docking in order to optimise hydrogen bonding interactions of these residues with the ligand. The positions of lysine NH3+ groups are similarly optimised. The starting positions of Ser, Thr and Tyr OH groups and Lys NH3+ groups therefore do not matter.
In cases where you are docking a ligand into a binding site known to contain a flexible side chain, it is possible to specify that this residue be allowed to undergo torsional rotation around one or more of its acyclic bonds. Up to ten rotatable side chains can be specified in this way. The conformation of the flexible torsion or torsions will be altered during docking (within user-defined boundaries) to optimise the H-bonding interactions of the residue with the ligand. The side chains that are required to rotate are easily defined via the GOLD Setup interface. The movements of residues allowed to rotate during docking can be viewed in Hermes and the optimised torsion values can be found in the gold_ligand.log file. Further information about this feature and how to use it can be found in the GOLD documentation.
Where multiple models of the protein are available it is recommended to use the Ensemble Docking option in order to dock to these multiple protein models simultaneously and competitively. This is the recommended way to take account of backbone flexibility in proteins with GOLD.