Automatic prediction of protein interactions with large scale motion

Proteins often change their conformation upon binding to other molecules. Taking these conformational changes into account in docking is an extremely difficult task: the larger the scale of the motion the harder it is to predict the structure of the association complex. Here, we present a fully automated method for flexible docking with large scale motion in one of the docked molecules. The method automatically identifies hinge regions and rigid parts and then docks the input mole cules while explicitly consider ing the hinges and possible protein motions.