Does MVD support flexible ligands and/or receptor flexibility?
The optimal position, rotation, and torsion angles of rotatable bonds are determined during the docking run. The rotatable bonds are single bond not part of a ring. Bonds can be chosen to be held fixed during docking (allowing for partial or fully rigid docking). Ring conformations and bond lengths are not changed during the docking simulation. In order to investigate different ring conformations a molecular modeling tool should be used, and a few of the conformations with lowest energy should be docked. It is possible to simulate ‘induced fit’ effects during the docking simulation: in MVD this is done by softening the potential during the docking (by increasing the tolerance of the PLP-potentials or by weakening selected sidechains interactions), docking a diverse set of poses, and finally optimizing the sidechain configurations. Notice that the backbone atoms of the protein will be held fixed – only the sidechain angles are changed.
