Database of Molecular Motions explained

Database of Macromolecular Motions
Author:	Mark B. Gerstein Werner G. Krebs
Developer:	molmovdb.org team at Yale University
Genre:	bioinformatics database, Software as a service

The Database of Macromolecular Motions is a bioinformatics database and software-as-a-service tool that attempts tocategorize macromolecular motions, sometimes also known as conformational change.^{[1] [2] [3]} It was originally developed by Mark B. Gerstein, Werner Krebs, and Nat Echols in the Molecular Biophysics & Biochemistry Department at Yale University.^{[4] [5]}

Discussion

Since its introduction in the late 1990s, peer-reviewed papers on the database have received thousands of citations.^{[6] [7]} The database has been mentioned in news articles in major scientific journals, book chapters, and elsewhere.

Users can search the database for a particular motion by either protein name or Protein Data Bank ID number.^[8] 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. This system uses molecular modelling techniques to interpolate the structural changes between two different protein conformers and to generate a set of intermediate structures. A hyperlink pointing to the morph results is then emailed to the user.^[9]

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.^[10] Since their initial introduction in 1996, the database and associated morph server have undergone development to try to address some of these shortcomings^{[11] [12]} as well as add new features, such as Normal Mode Analysis.^[13] Other research grounds have subsequently developed alternative systems, such as MovieMaker from the University of Alberta.^[10]

Commercialization

Bioinformatics vendor DNASTAR has incorporated morphs from the database into its commercial Protean3D product.^{[14] [15]} The connection between DNASTAR and the authors of the database, if any, is not immediately clear.

See also

• Database of protein conformational diversity

Notes

• Book: Gu. Jenny. Bourne. Philip E.. Structural Bioinformatics. 2nd . Wiley-Blackwell. March 2009. 978-0-470-18105-8.
• Book: 978-1441910431. Chapter 26 on Protein Motions. The Physics of Proteins: An Introduction to Biological Physics and Molecular Biophysics (Biological and Medical Physics, Biomedical Engineering). Frauenfelder. Hans. 10 June 2010. Springer .
• Frauenfelder H . New looks at protein motions . Nature . 338 . 6217. 623–4 . 20 April 1989 . 10.1038/338623a0 . 1989Natur.338..623F . 33628943 .
• 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. . 14 . 3 . 633–43 . March 2005 . 15722444 . 2279292 . 10.1110/ps.04882105 .
• Alexandrov V, Gerstein M . Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures . BMC Bioinformatics . 5. 2 . January 2004 . 14715091 . 344530 . 10.1186/1471-2105-5-2 . free .
• Echols N, Milburn D, Gerstein M . MolMovDB: analysis and visualization of conformational change and structural flexibility . Nucleic Acids Res. . 31 . 1 . 478–82 . January 2003 . 12520056 . 165551 . 10.1093/nar/gkg104.
• Krebs WG, Alexandrov V, Wilson CA, Echols N, Yu H, Gerstein M . 1132091 . Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic . Proteins . 48 . 4 . 682–95 . September 2002 . 12211036 . 10.1002/prot.10168 .

External links

• The Database of Macromolecular Motions (molmovdb)
• MovieMaker from the University of Alberta

Notes and References

1. Hot Picks. Science. 1999-05-07. 0036-8075. 871b–871. 284. 5416. 10.1126/science.284.5416.871b. 220104660. en.
2. Book: Structural Bioinformatics . limited . Bourne PE, Helge W . 2003 . Hoboken, NJ . Wiley-Liss . 978-0-471-20199-1 . 50199108. 229.
3. Bourne, PE . Murray-Rust, J . Lakey JH . Protein-nucleic acid interactions Folding and binding Web alert . Current Opinion in Structural Biology . 9 . 1. 9–10 . Feb 1999. 10.1016/S0959-440X(99)90000-3.
4. Web site: Morphs. Proteopeida. 2015-10-30.
5. Borner. Knowledge Management and Visualization Tools in Support of Discovery (NSF Workshop Report). National Science Foundation Workshop. 5. 2015-12-26. https://web.archive.org/web/20160304101330/http://vw.slis.indiana.edu/cdi2008/NSF-Report.pdf. 2016-03-04. dead.
6. Web site: Mark Gerstein - Google Scholar Citations. scholar.google.com. 2015-12-26.
7. Web site: Werner G. Krebs - Google Scholar Citations. scholar.google.com. 2015-12-26.
8. Gerstein M, Krebs W . A database of macromolecular motions . Nucleic Acids Res. . 26 . 18 . 4280–90 . September 1998 . 9722650. 147832 . 10.1093/nar/26.18.4280.
9. Krebs WG, Gerstein M . SURVEY AND SUMMARY: The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework . Nucleic Acids Res. . 28 . 8 . 1665–75 . April 2000 . 10734184 . 102811 . 10.1093/nar/28.8.1665.
10. Maiti R, Van Domselaar GH, Wishart DS . MovieMaker: a web server for rapid rendering of protein motions and interactions . Nucleic Acids Res. . 33 . Web Server issue . W358–62 . July 2005 . 15980488 . 1160245 . 10.1093/nar/gki485 .
11. 16381870. 1347409. The Database of Macromolecular Motions: new features added at the decade mark. Nucleic Acids Research. 34. Database issue. D296–301. 2006. Flores. S. Echols. N. Milburn. D. Hespenheide. B. Keating. K. Lu. J. Wells. S. Yu. E. Z.. Thorpe. M. Gerstein. M. 10.1093/nar/gkj046.
12. Alexandrov V, Gerstein M . Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures . BMC Bioinformatics . 5. 2 . January 2004 . 14715091 . 344530 . 10.1186/1471-2105-5-2 . free .
13. 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. . 14 . 3 . 633–43 . March 2005 . 15722444 . 2279292 . 10.1110/ps.04882105 .
14. Web site: The Motion Library in Protean3D documentation. www.dnastar.com. 2015-11-13.
15. Web site: Protean3D overview. www.dnastar.com. 2015-11-13.