Comparing bound and unbound protein structures using energy calculation and rotamer statistics

Koch K, Zöllner F, Neumann S, Kummert F, Sagerer G. Comparing bound and unbound protein structures using energy calculation and rotamer statistics. In Silico Biology. 2002;2(3):32-32.Protein data in the PDB covers only a snapshot of a protein structure. For flexible docking conformational changes need to be considered. Rotamer statistics provide the likelihood for side chain conformations, and further comparison of bound and unbound state yields differences in preferred positions. Furthermore, we do a full sampling of selected Chi angles and apply the AMBER force field. Conformation of energy minima comply with the rotamer statistics. Both types of information target the reduction of search space for enumerative docking algorithms and provide parameters for elastic docking. Key words: Rotamer library, flexible protein-protein docking, energy calculations, AMBER force field, side chain flexibility, flexibility measur