Does GOLD allow for protein flexibility?
GOLD allows for partial protein flexibility in all dockings. Specifically GOLD rotates the torsion angles of Ser, Thr and Tyr hydroxyl groups during docking in order to optimise H-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 interface. This feature is available for the GoldScor
