Database of Molecular Motions
The Database of Macromolecular Motions is a bioinformatics computer database on the Internet. It attempts to divide motions of protein and some RNA biological molecules into different types.[1][2]
Description
changeIt was originally made by Mark B. Gerstein, Werner G. Krebs and Nat Echols in the molecular biophysics and biochemistry group at Yale University. People can use an Internet page to search this computer database for a particular motion by either the protein name or Protein Data Bank number. However, many people find this computer database by just coming over from the Internet page for the protein entry at the Protein Data Bank. For proteins found in both computer databases, this different computer database often gives a link back to the Internet page for the protein on this Internet site.
The computer database includes an Internet tool or free Software as a service (the "Morph server") which lets non-experts see certain protein motions through the generation of short motion pictures. The motion pictures are made automatically by computer software on the Internet site. When done the Internet site sends an email with the motion picture information back to the user.[3]
The "Morph Server" tool was originally a research tool rather than a tool for making motion pictures, and thus offered only limited user control over rendering, color, and point of view, and the original method sometimes required a fair amount of computer time to complete.[4] Since the site's initial introduction in 1996, the Internet site has been made better to try to fix some of these issues[5] as well as add new things.[6] Other people have now made alternative systems, such as MovieMaker Archived 2016-01-24 at the Wayback Machine from the University of Alberta.[4]
References
change- ↑ "Hot Picks". Science. 284 (5416): 871. 1999-05-07. doi:10.1126/science.284.5416.871b. ISSN 0036-8075. S2CID 220104660.
- ↑ 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.
- ↑ Krebs WG, Gerstein M (April 2000). "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. doi:10.1093/nar/28.8.1665. PMC 102811. PMID 10734184.
- ↑ 4.0 4.1 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.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ↑ 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.
- ↑ 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.
{{cite journal}}: CS1 maint: multiple names: authors list (link)
Other websites
change- The Database of Macromolecular Motions (molmovdb)
- Book Chapter on Protein Motions Archived 2008-10-11 at the Wayback Machine from website of RH Austin Archived 2016-03-04 at the Wayback Machine at Princeton University
- Frauenfelder H (20 April 1989). "New looks at protein motions". Nature. 338 (6217): 623–4. doi:10.1038/338623a0. S2CID 33628943.
- 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.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - 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.
- 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.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - 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. S2CID 1132091.
{{cite journal}}: CS1 maint: multiple names: authors list (link)