Database of Molecular Motions

The Database of Macromolecular Motions (molmovdb) [1] is a bioinformatics database that attempts to categorize macromolecular motions, sometimes also known as conformational change [2]. It was original developed by Mark B. Gerstein, Samuel Flores, Werner Krebs, and Nat Echols in the Molecular Biophysics & Biochemistry Department at Yale University.

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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 [3].

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 [4]. Since their initial introduction in 1996, the database and associated morph server have undergone development to try to address some of these shortcomings [5] as well as add new features, such as Normal Mode Analysis [6]. Other research grounds have subsequently developed alternative systems, such as MovieMaker [7] from the University of Alberta [8].

Book Chapter on Protein Motions from website of RH Austin [9] at Princeton University

[PMID 9722650] Gerstein M, Krebs W (1998). A database of macromolecular motions. Nucleic Acids Res. 1998 Sep 15;26(18):4280-90.

[PMID 10734184] Krebs WG, Gerstein M (2000). The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework. Nucleic Acids Res. 2000 Apr 15;28(8):1665-75.

Frauenfelder, H. New looks at protein motions Nature 338, 623 - 624 (20 April 1989).

[PMID 1160245] Flores S, Echols N, Milburn D, Hespenheide B, Keating K, Lu J, Wells S, Yu EZ, Thorpe M, Gerstein M (2006). The Database of Macromolecular Motions: new features added at the decade mark.Nucleic Acids Res. 2006 Jan 1;34(Database issue):D296-301

[PMID 15722444] Alexandrov V, Lehnert U, Echols N, Milburn D, Engelman D, Gerstein M. Normal modes for predicting protein motions: a comprehensive database assessment and associated Web tool. Protein Sci. 2005 Mar;14(3):633-43.

[PMID 14715091] Alexandrov V and Gerstein M. Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures. BMC Bioinformatics. 2004 Jan 9;5:2

[PMID 12520056] Echols N, Milburn D, Gerstein M (2003). MolMovDB: analysis and visualization of conformational change and structural flexibility. Nucleic Acids Res. 2003 Jan 1;31(1):478-82.

[PMID 12211036] Krebs WG,Alexandrov V, Wilson CA, Echols N, Yu H, Gerstein M (2002). Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic. Proteins. 2002 Sep 1;48(4):682-95.

[PMID 1160245] Maiti R, Van Domselaar G H, Wishart D S, MovieMaker: a web server for rapid rendering of protein motions and interactions, Nucleic Acids Res. 2005 July 1; 33(Web Server issue): W358–W362.