Web portal to an image database for high-resolution three-dimensional reconstruction

Journal of Structural Biology

Volumn 144, Issue 1-2, 2003, Pages 238-245

  Dai, Wei ^a,b   Liang, Yuyao ^b   Zhou, Z Hong ^a,b  

^a UNIVERSITY OF TEXAS   (United States)

^b UNIVERSITY OF TEXAS MEDICAL SCHOOL   (United States)

Author keywords

Active server pages (ASP); Chart tools; Data entry; Data reporting; Image database; SQL; User management; Web portal

Indexed keywords

ARTICLE; DATA ANALYSIS; HUMAN COMPUTER INTERACTION; IMAGE ANALYSIS; IMAGE RECONSTRUCTION; INFORMATION PROCESSING; INTERNET; PRIORITY JOURNAL; SYSTEM ANALYSIS; THREE DIMENSIONAL IMAGING;

EID: 0344983333     PISSN: 10478477     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jsb.2003.09.035     Document Type: Article

References (34)

1. Albini G., Falque M., Joets J. ActionMap: a web-based software that automates loci assignments to framework maps. Nucleic Acids Res. 31:2003;3815-3818.
2. Asare A.L., Huda H., Klimczak J.C., Caldwell C.W. Integrating molecular diagnostic and flow cytometric reporting for improved longitudinal monitoring of HIV patients. Proc. AMIA Symp. 1998;952-956.
3. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The Protein Data Bank. Nucleic Acids Res. 28:2000;235-242.
4. Bhamidipati K. SQL Programmer's Reference. 1998;Osborne/McGraw-Hill, Berkeley, CA.
5. Böttcher B., Wynne S.A., Crowther R.A. The fold of the core protein of hepatitis B virus determined by electron cryomicroscopy. Hitachi Instrument News (Electron Microscopy Edition). 32:1997;3-8.
6. Carazo J.M., Stelzer E.H., Engel A., Fita I., Henn C., Machtynger J., McNeil P., Shotton D.M., Chagoyen M., de Alarcon P.A., Fritsch R., Heymann J.B., Kalko S., Pittet J.J., Rodriguez-Tome P., Boudier T., Marabini R., Vaquerizo C., Fernandez J.J., Frank J. Organising multi-dimensional biological image information: the BioImage Database Proposal for a new distributed database of macromolecular and subcellular structures from different areas of microscopy. Nucleic Acids Res. 27:1999;280-283.
7. Conway J.F., Cheng N., Zlotnick A., Wingfield P.T., Stahl S.J., Steven A.C. Visualization of a 4-helix bundle in the hepatitis B virus capsid by cryo-electron microscopy. Nature. 386:1997;91-94.
8. de Alarcon P.A., Gupta A., Carazo J.M. A framework for querying a database for structural information on 3D images of macromolecules: a web-based query-by-content prototype on the BioImage macromolecular server. J. Struct. Biol. 125:1999;112-122.
9. Fellmann D., Pulokas J., Milligan R.A., Carragher B., Potter C.S. A relational database for cryoEM: experience at one year and 50,000 images. J. Struct. Biol. 137:2002;273-282.
10. Gabashvili I.S., Agrawal R.K., Spahn C.M., Grassucci R.A., Svergun D.I., Frank J., Penczek P. Solution structure of the E. coli 70S ribosome at 11.5. Å Cell. 100:2000;537-549.
11. Golas M.M., Sander B., Will C.L., Luhrmann R., Stark H. Molecular architecture of the multiprotein splicing factor SF3b. Science. 300:2003;980-984.
12. Grundy W.N., Bailey T.L. Family pairwise search with embedded motif models. Bioinformatics. 15:1999;463-470.
13. He J., Schmid M.F., Zhou Z.H., Rixon F., Chiu W. Finding and using local symmetry in identifying lower domain movements in hexon subunits of the herpes simplex virus type 1 b capsid. J. Mol. Biol. 309:2001;903-914.
14. Henderson R. The potential and limitations of neutrons, electrons and X-rays for atomic resolution microscopy of unstained biological molecules. Q. Rev. Biophys. 28:1995;171-193.
15. Jensen G.J. Alignment error envelopes for single particle analysis. J. Struct. Biol. 133:2001;143-155.
16. Joubert M., Aymard S., Staccini P., Fieschi M. Designing and implementing medical web portals: spreading educational and research materials on the Internet. Proc. AMIA Symp. 2001;299-303.
17. Kalko S.G., Chagoyen M., Jimenez-Lozano N., Verdaguer N., Fita I., Carazo J.M. The need for a shared database infrastructure: combining X-ray crystallography and electron microscopy. Eur. Biophys. J. 29:2000;457-462.
18. Lenhard B., Hayes W.S., Wasserman W.W. GeneLynx: a gene-centric portal to the human genome. Genome Res. 11:2001;2151-2157.
19. Li H., DeRosier D.J., Nicholson W.V., Nogales E., Downing K.H. Microtubule structure at 8. Å resolution Structure (Camb). 10:2002;1317-1328.
20. Liang Y., Ke E.Y., Zhou Z.H. IMIRS: a high-resolution 3D reconstruction package integrated with a relational image database. J. Struct. Biol. 137:2002;292-304.
21. Martone M.E., Gupta A., Wong M., Qian X., Sosinsky G., Ludascher B., Ellisman M.H. A cell-centered database for electron tomographic data. J. Struct. Biol. 138:2002;145-155.
22. Matadeen R., Patwardhan A., Gowen B., Orlova E.V., Pape T., Cuff M., Mueller F., Brimacombe R., van Heel M. The Escherichia coli large ribosomal subunit at 7.5. Å resolution Structure Fold Des. 7:1999;1575-1583.
23. Meissner U., Stohr M., Kusche K., Burmester T., Stark H., Harris J.R., Orlova E.V., Markl J. Quaternary structure of the European spiny lobster (Palinurus elephas) 1x6-mer hemocyanin from cryoEM and amino acid sequence data. J. Mol. Biol. 325:2003;99-109.
24. Metoz F., Sherman M.B., Schmid M.F. Adopting a database as a solution to managing electron image data. J. Struct. Biol. 133:2001;170-175.
25. Nielsen J. Designing User Interfaces for International Use. 1990;Elsevier, Amsterdam, New York.
26. Nielsen J. Designing Web Usability. 2000;New Riders, Indianapolis, IN.
27. Palamas S., Kalivas D., Panou-Diamandi O., Zeelenberg C., van Nimwegen C. Design and implementation of a portal for the medical equipment market: MEDICOM. J. Med. Internet Res. 3:2001;E32.
28. Poirot O., O'Toole E., Notredame C. Tcoffee@igs: a web server for computing, evaluating and combining multiple sequence alignments. Nucleic Acids Res. 31:2003;3503-3506.
29. Shepker M. Writing Stored Procedures for Microsoft SQL Server. 2000;SAMS, Indianapolis, IN.
30. van Kampen A.H., van Schaik B.D., Pauws E., Michiels E.M., Ruijter J.M., Caron H.N., Versteeg R., Heisterkamp S.H., Leunissen J.A., Baas F., van der Mee M. USAGE: a web-based approach towards the analysis of SAGE data. Serial Analysis of Gene Expression. Bioinformatics. 16:2000;899-905.
31. Zhou Z.H., Baker M.L., Jiang W., Dougherty M., Jakana J., Dong G., Lu G., Chiu W. Electron cryomicroscopy and bioinformatics suggest protein fold models for rice dwarf virus. Nat. Struct. Biol. 8:2001;868-873.
32. Zhou Z.H., Chiu W. Determination of icosahedral virus structures by electron cryomicroscopy at subnanometer resolution. Chiu W., Johnson J. Advances in Protein Chemistry. vol. 64:2003;93-124 Elsevier/Academic Press, St. Louis, MO, USA.
33. Zhou Z.H., Dougherty M., Jakana J., He J., Rixon F.J., Chiu W. Seeing the herpesvirus capsid at 8.5. Å Science. 288:2000;877-880.
34. Zhou Z.H., Zhang H., Jakana J., Lu X.-Y., Zhang J.-Q. Cytoplasmic polyhedrosis virus structure at 8. Å by electron cryomicroscopy: structural basis of capsid stability and mRNA processing regulation Structure. 11:2003;651-663.