A DATABASE OF MACROMOLECULAR MOTIONS

We describe a database of macromolecular motions meant to be of genera l use to the structural community. The database, which is accessible o n the World Wide Web with an entry point at http://bioinfo.mbb.yale.ed u/ MolMovDB,attempts to systematize all instances of protein and nucle ic acid movement for which there is at least some structural informati on. At present it contains >120 motions, most of which are of proteins . Protein motions are further classified hierarchically into a limited number of categories, first on the basis of size (distinguishing betw een fragment, domain and subunit motions) and then on the basis of pac king. Our packing classification divides motions into various categori es (shear, hinge, other) depending on whether or not they involve slid ing over a continuously maintained and tightly packed interface. In ad dition, the database provides some indication about the evidence behin d each motion (i.e. the type of experimental information or whether th e motion is inferred based on structural similarity) and attempts to d escribe many aspects of a motion in terms of a standardized nomenclatu re (e.g. the maximum rotation, the residue selection of a fixed core, etc.). Currently, we use a standard relational design to implement the database. However, the complexity and heterogeneity of the informatio n kept in the database makes it an ideal application for an object-rel ational approach, and we are moving it in this direction. Specifically , in terms of storing complex information, the database contains plaus ible representations for motion pathways, derived from restrained 3D i nterpolation between known endpoint conformations. These pathways can be viewed in a variety of movie formats, and the database is associate d with a server that can automatically generate these movies from subm itted coordinates.