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.^[1] 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.^[2]

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 sometimes required a fair amount of CPU time to completion.^[3] Since their initial introduction in 1996, the database and associated morph server have undergone development to try to address some of these shortcomings ^[4] as well as add new features, such as Normal Mode Analysis.^[5] Other research grounds have subsequently developed alternative systems, such as MovieMaker from the University of Alberta.^[3]

External links

• The Database of Macromolecular Motions (molmovdb)
• Book Chapter on Protein Motions from website of RH Austin at Princeton University
• Frauenfelder H (20 April 1989). "New looks at protein motions". Nature 338 (6217): 623–4. doi:10.1038/338623a0. http://www.nature.com/nature/journal/v338/n6217/abs/338623a0.html. 
• Alexandrov V, Lehnert U, Echols N, Milburn D, Engelman D, Gerstein M (March 2005). "Normal modes for predicting protein motions: a comprehensive database assessment and associated Web tool". Protein Sci. 14 (3): 633–43. doi:10.1110/ps.04882105. PMC 2279292. PMID 15722444. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2279292. 
• Alexandrov V, Gerstein M (January 2004). "Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures". BMC Bioinformatics 5: 2. doi:10.1186/1471-2105-5-2. PMC 344530. PMID 14715091. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=344530. 
• Echols N, Milburn D, Gerstein M (January 2003). "MolMovDB: analysis and visualization of conformational change and structural flexibility". Nucleic Acids Res. 31 (1): 478–82. doi:10.1093/nar/gkg104. PMC 165551. PMID 12520056. http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=12520056. 
• Krebs WG, Alexandrov V, Wilson CA, Echols N, Yu H, Gerstein M (September 2002). "Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic". Proteins 48 (4): 682–95. doi:10.1002/prot.10168. PMID 12211036. 

See also

• Database of protein conformational diversity

References

1. ^ Gerstein M, Krebs W (September 1998). "A database of macromolecular motions". Nucleic Acids Res. 26 (18): 4280–90. doi:10.1093/nar/26.18.4280. PMC 147832. PMID 9722650. http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=9722650. 
2. ^ Krebs WG, Gerstein M (April 2000). "The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework". Nucleic Acids Res. 28 (8): 1665–75. doi:10.1093/nar/28.8.1665. PMC 102811. PMID 10734184. http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=10734184. 
3. ^ ^{a b} Maiti R, Van Domselaar GH, Wishart DS (July 2005). "MovieMaker: a web server for rapid rendering of protein motions and interactions". Nucleic Acids Res. 33 (Web Server issue): W358–62. doi:10.1093/nar/gki485. PMC 1160245. PMID 15980488. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1160245. 
4. ^ Alexandrov V, Gerstein M (January 2004). "Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures". BMC Bioinformatics 5: 2. doi:10.1186/1471-2105-5-2. PMC 344530. PMID 14715091. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=344530. 
5. ^ Alexandrov V, Lehnert U, Echols N, Milburn D, Engelman D, Gerstein M (March 2005). "Normal modes for predicting protein motions: a comprehensive database assessment and associated Web tool". Protein Sci. 14 (3): 633–43. doi:10.1110/ps.04882105. PMC 2279292. PMID 15722444. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2279292.