An aggregate analysis of many predicted structures to reduce errors in protein structure comparison caused by conformational flexibility

Background Conformational flexibility creates errors in the comparison of protein structures. Even small changes in backbone or sidechain conformation can radically alter the shape of ligand binding cavities. These changes can cause structure comparison programs to overlook functionally related proteins with remote evolutionary similarities, and cause others to incorrectly conclude that closely related proteins have different binding preferences, when their specificities are actually similar. Towards the latter effort, this paper applies protein structure prediction algorithms to enhance the classification of homologous proteins according to their binding preferences, despite radical conformational differences.