Studying Macromolecular Motions in a Database Framework: From Structure to Sequence

Abstract

of Voronoi polyhedra and Delaunay triangulation. In addition to the packing classification, the database provides some indication about the evidence behind each motion (i.e. the type of experimental information or whether the motion is inferred based on structural similar- ity) and attempts to describe many aspects of a motion in terms of a standardized nomen- clature (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 information kept in the database makes it an ideal application for an object-relational approach, and we are moving it in this direction. The database, moreover, incorporates innovative Internet cooperatively features that allow authorized remote ex- perts to serve as database editors. The database also contains plausible representations for 1 motion pathways, derived from restrained 3D interpolation between known endpoint con- formations. These pathways can be viewed in a variety of movie formats, and the database is associated with a server that can automatically generate these movies from submitted coordinates. Based on the structures in the database we have developed sequence patterns for linkers and flexible hinges and are currently using these for the annotation of genome sequence data.