Database of Molecular Motions

The Database of Macromolecular Motions (molmovdb) is a bioinformatics database that attempts to categorize macromolecular motions, sometimes also known as conformational change. It was original developed by Mark B. Gerstein, Samuel Flores, Werner Krebs, and Nat Echols in the Molecular Biophysics & Biochemistry Department at Yale University.

Users can search the database for a particular motion by either protein name or Protein Data Bank ID number. Typically, however, users will enter the database via the Protein Data Bank, which often provides a hyperlink to the molmovdb entry for proteins found in both databases.

The database includes a web-based tool (the Morph server) which allows non-experts to animate and visualize certain types of protein conformational change through the generation of short movies (8). This system uses molecular modelling techniques to interpolate the structural changes between two different protein conformers and to generate a set of plausible intermediate structures. A hyperlink pointing to the morph results is then emailed to the user.

The Morph Server was originally primarily a research tool rather than general molecular animation tool, and thus offered only limited user control over rendering, animation parameters, color, and point of view, and the original methods sometimed required a fair amount of CPU time to completion. Since their initial introduction in 1996, the database and associated morph server have undergone development to try to address some of these shortcomings as well as add new features, such as Normal Mode Analysis. Other research grounds have subsequently developed alternative systems, such as MovieMaker from the University of Alberta.