The Morph Server and the Macromolecular Motions Database: a standardized system for analyzing and visualizing macromolecular motions in a database framework

The number of solved structures of macromolecules that have the same fold and thus exhibit some degree of conformational variability is rapidly increasing. It is consequently advantageous to develop a standardized terminology for describing this variability and automated systems for processing protein structures in di erent conformations. We have developed such a system as a 'front-end' server to our database of macromolecular motions, a database that classi es proteins into a limited number of categories, rst on the basis of size (distinguishing between fragment, domain, and subunit motions) and then on the basis of packing. Our system attempts to describe a protein motion as a rigid-body rotation of a small 'core' relative to a larger one, using a set of hinges. The motion is placed in a standardized coordinate system so that all statistics between any two motions are directly comparable. We nd that while this model can accommodate most protein motions, it cannot accommodate all; the degree to which a motion can be accommodated provides