Proteopedia: A status report on the collaborative, 3D web-encyclopedia of proteins and other biomolecules

Journal of Structural Biology

Volumn 175, Issue 2, 2011, Pages 244-252

  Prilusky, Jaime ^a   Hodis, Eran ^a,f   Canner, David ^a,b   Decatur, Wayne A ^c   Oberholser, Karl ^d   Martz, Eric ^e   Berchanski, Alexander ^a   Harel, Michal ^a   Sussman, Joel L ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^b Chemistry Department   (United States)

^c UNIVERSITY OF NEW HAMPSHIRE   (United States)

^d MESSIAH COLLEGE   (United States)

^e UNIVERSITY OF MASSACHUSETTS   (United States)

^f BROAD INSTITUTE OF MIT AND HARVARD   (United States)

Author keywords

3D Molecular visualization; Structure function; Web encyclopedia; Wiki

Indexed keywords

PROTEIN;

ARTICLE; COMPUTER PROGRAM; INFORMATION PROCESSING; INFORMATION SYSTEM; PEDAGOGICS; PRIORITY JOURNAL; PROTEIN DATA BANK; PROTEOPEDIA;

ENCYCLOPEDIAS AS TOPIC; INFORMATION DISSEMINATION; INFORMATION MANAGEMENT; INFORMATION SERVICES; MODELS, MOLECULAR; MOLECULAR BIOLOGY; ONLINE SYSTEMS; PROTEIN CONFORMATION; PROTEINS; USER-COMPUTER INTERFACE;

EID: 79959942896     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2011.04.011     Document Type: Article

References (35)

1. Abagyan R., Lee W.H., Raush E., Budagyan L., Totrov M., et al. Disseminating structural genomics data to the public: from a data dump to an animated story. TIBS 2006, 31:76-78.
2. Accelrys, 2008, Discovery Studio Visualizer 2.0, http://accelrys.com/products/discovery-studio/visualization/discovery-studio-visualizer.html.
3. Banci, L., Bertini, I., Ciofi-Baffoni, S., Kozyreva, T., Mori, M., et al., 2011. Sco proteins are involved in electron transfer processes. J. Biol. Inorg. Chem. (ePub).
4. Berman H., Henrick K., Nakamura H., Markley J.L. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res. 2007, 35:D301-D303.
5. Canner D. Proteopedia entry: HMG-CoA reductase. Biochem. Mol. Biol. Educ. 2011, 39:64.
6. Decatur W.A. Proteopedia entry: the large ribosomal subunit of Haloarcula marismortui. Biochem. Mol. Biol. Educ. 2010, 38:343.
7. Dym O., Albeck S., Unger T., Jacobovitch J., Branzburg A., et al. Crystal structure of the Agrobacterium virulence complex VirE1-VirE2 reveals a flexible protein that can accommodate different partners. PNAS 2008, 105:11170-11175.
8. Flores S., Echols N., Milburn D., Hespenheide B., Keating K., et al. The database of macromolecular motions: new features added at the decade mark. Nucleic Acids Res. 2006, 34:D296-301.
9. Hanson R. Jmol - a paradigm shift in crystallographic visualization. J. Appl. Cryst. 2010, 43:1250-1260.
10. Herman, T., 2006. SMART (Students Modeling A Research Topic) Teams http://cbm.msoe.edu/stupro/smart.
11. Hodis E., Prilusky J., Martz E., Silman I., Moult J., et al. Proteopedia - a scientific 'wiki' bridging the rift between 3D structure and function of biomacromolecules. Genome Biol. 2008, 9:R121.
12. Igarashi J., Kobayashi K., Matsuoka A. A hydrogen-bonding network formed by the B10-E7-E11 residues of a truncated hemoglobin from Tetrahymena pyriformis is critical for stability of bound oxygen and nitric oxide detoxification. J. Biol. Inorg. Chem. 2011, 16:599-609.
13. Jmol, 2010. Jmol: An Open-Source Java Viewer for Chemical Structures in 3D. http://www.jmol.org.
14. Kalodimos C.G., Biris N., Bonvin A.M., Levandoski M.M., Guennuegues M., et al. Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Science 2004, 305:386-389.
15. Kendrew J.C., Bodo G., Dintzis H.M., Parrish R.G., Wyckoff H., et al. A three-dimensional model of the myoglobin molecule obtained by X-ray analysis. Nature 1958, 181:662-666.
16. Kovalevskiy O.V., Solonin A.S., Antson A.A. Structural investigation of transcriptional regulator HlyIIR: influence of a disordered region on protein fold and dimerization. Proteins 2010, 78:1870-1877.
17. Krebs W.G., Gerstein M. The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework. Nucleic Acids Res. 2000, 28:1665-1675.
18. Kumar P., Ziegler A., Grahn A., Hee C.S. Leaving the structural ivory tower, assisted by interactive 3D PDF. TIBS 2010, 35:419-422.
19. Kumar P., Ziegler A., Ziegler J., Uchanska-Ziegler B., Ziegler A. Grasping molecular structures through publication-integrated 3D models. TIBS 2008, 33:408-412.
20. Landau M., Mayrose I., Rosenberg Y., Glaser F., Martz E., et al. ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res. 2005, 33:W299-W302.
21. Lee W.H., Atienza-Herrero J.N., Abagyan R., Marsden B.D. SGC - structural biology and human health: a new approach to publishing structural biology results. PLoS One 2009, 4:e7675.
22. Marcey, D., 2011. The Online Macromolecular Museum, http://www.callutheran.edu/Academic_Programs/Departments/BioDev/omm/gallery.htm.
23. Martz, E., 2006. FirstGlance in Jmol. http://firstglance.jmol.org.
24. Martz, E., 2010. Molecular Visualization Resources. http://MolviZ.Org.
25. McMahon B., Hanson R.M. A toolkit for publishing enhanced figures. J. Appl. Cryst. 2008, 41:811-814.
26. MediaWiki, 2007. http://www.mediawiki.org.
27. Oberholser K. Proteopedia entry: Ramachandran plots. Biochem. Mol. Biol. Educ. 2010, 38:430.
28. Pace H.C., Lu P., Lewis M. Lac repressor: crystallization of intact tetramer and its complexes with inducer and operator DNA. PNAS 1990, 87:1870-1873.
29. Palmer A.G., Matthews B.W. Interactive graphics return to protein science. Protein Sci. 2009, 18:677.
30. Prilusky, J., 1996. OCA, a browser-database for protein structure/function. http://oca.weizmann.ac.il/oca-docs/oca-home.html.
31. Reichsman, F., 2010. Molecules in Motion. http://www.moleculesinmotion.com.
32. Richardson D.C., Richardson J.S. The kinemage: a tool for scientific communication. Protein Sci. 1992, 1:3-9.
33. Slonczewski, J., 2009. Biomolecules at Kenyon. http://biology.kenyon.edu/BMB/biomolecules.htm.
34. Sussman J.L., Lin D., Jiang J., Manning N.O., Prilusky J., et al. The protein data bank at Brookhaven. International Tables for Crystallography. Volume F. Crystallography of Biological Macromolecules 2001, 649-656. Kluwer Academic Publishers, Dordrecht. M.G. Rossmann, E. Arnold (Eds.).
35. Wang F., Herzig C.T., Chen C., Hsu H., Baldwin C.L., et al. Scavenger receptor WC1 contributes to the gammadelta T cell response to Leptospira. Mol. Immunol. 2011, 48:801-809.