VRDD: applying virtual reality visualization to protein docking and design.

摘要: We have developed an interactive docking program called VRDD. It offers various modes of displaying molecules in immersive, three-dimensional virtual reality (VR) environment. allows a user to interactively perform molecular aided by automatic and side chain conformational search. Binding free energies are computed real time, the enables explore only clash-free orientations ligand. VRDD also supplies visual auditory feedback during search, indicating levels atomic overlap interaction energy. The stunning VR graphics immerse users scene can maximally stimulate their design intuition. tested on three cases with increasing complexity: nine-residue-long peptide bound major histocompatibility complex (MHC) molecule, barstar barnase, antibody hemagglutinin. Without prior knowledge, combinations hand-docking refinement led accurate structures for first two complexes. third case, which all algorithms failed identify correct previous blind test, Our results show that combination make unique contributions modeling.