The distribution and query systems of the RCSB Protein Data Bank

Nucleic Acids Research

Volumn 32, Issue DATABASE ISS., 2004, Pages

  Bourne, Philip E ^a,b   Addess, Kenneth J ^a   Bluhm, Wolfgang F ^a   Chen, Li ^c   Deshpande, Nita ^a   Feng, Zukang ^c   Fleri, Ward ^a   Green, Rachel ^c   Merino Ott, Jeffrey C ^a   Townsend Merino, Wayne ^a   Weissig, Helge ^d   Westbrook, John ^c   Berman, Helen M ^c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c RUTGERS UNIVERSITY   (United States)

^d ACTIVX BIOSCIENCES INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID;

AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; COMPUTER; COMPUTER PROGRAM; CRYOELECTRON MICROSCOPY; INFORMATION RETRIEVAL; INFORMATION SYSTEM; INTERNET; MACROMOLECULE; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN DATA BANK; PROTEIN STRUCTURE; X RAY CRYSTALLOGRAPHY;

ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; HUMANS; INFORMATION STORAGE AND RETRIEVAL; INTERNET; PROTEINS; USER-COMPUTER INTERFACE;

EID: 9144251611     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (15)

1. Berman,H.M., Westbrook,J., Feng,Z., Gilliland,G., Bhat,T.N., Weissig,H., Shindyalov,I.N. and Bourne,P.E. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
2. Bernstein,F.C., Koetzle,T.F., Williams,G.J.B., Meyer,E.F.,Jr, Brice,M.D., Rodgers,J.R., Kennard,O., Shimanouchi,T. and Tasumi,M. (1977) Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol., 112, 535-542.
3. Bhat,T.N., Bourne,P., Feng,Z., Gilliland,G., Jain,S., Ravichandran,V., Schneider,B., Schneider,K., Thanki,N., Weissig,H. et al. (2001) The PDB data uniformity project. Nucleic Acids Res., 29, 214-218.
4. Westbrook,J., Feng,Z., Jain,S., Bhat,T.N., Thanki,N., Ravichandran,V., Gilliland,G.L., Bluhm,W., Weissig,H., Greer,D.S. et al. (2002) The Protein Data Bank: unifying the archive. Nucleic Acids Res., 30, 245-248.
5. Westbrook,J., Feng,Z., Chen,L., Yang,H. and Berman,H.M. (2003) The Protein Data Bank and structural genomics. Nucleic Acids Res., 31, 489-491.
6. Bourne,P.E., Berman,H.M., Watenpaugh,K., Westbrook,J.D. and Fitzgerald,P.M.D. (1997) The macromolecular Crystallographic Information File (mmCIF). Methods Enzymol., 277, 571-590.
7. Ashburner,M., Ball,C.A., Blake,J.A., Botstein,D., Butler,H., Cherry,J.M., Davis,A.P., Dolinski,K., Dwight,S.S., Eppig,J.T. et al. The Gene Ontology Consortium (2000) Gene Ontology: tool for the unification of biology. Nature Genet., 25, 25-29.
8. Shindyalov,I.N. and Bourne,P.E. (1997) Protein data representation and query using optimized data decomposition. Comput. Appl. Biosci., 13, 487-496.
9. Li,W., Jaroszewski,L. and Godzik,A. (2001) Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics, 17, 282-283.
10. Tate,J.G., Moreland,J.L. and Bourne,P.E. (2001) Design and implementation of a collaborative molecular graphics environment. J. Mol. Graph. Model., 19, 280-287, 369-373.
11. Neshich,G., Togawa,R.C., Mancini,A.L., Kuser,P.R., Yamagishi,M.E., Pappas,G.,Jr, Torres,W.V., Fonseca e Campos,T., Ferreira,L.L., Luna,F.M. et al. (2003) STING Millennium: a web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence. Nucleic Acids Res., 31, 3386-3392.
12. Guex,N., Diemand,A. and Peitsch,M.C. (1999) Protein modelling for all. Trends Biochem. Sci., 24, 364-367.
13. Henrick,K. and Thornton,J.M. (1998) PQS: a protein quaternary structure file server. Trends Biochem. Sci., 23, 358-361.
14. Boeckmann,B., Bairoch,A., Apweiler,R., Blatter,M.C., Estreicher,A., Gasteiger,E., Martin,M.J., Michoud,K., O'Donovan,C., Phan,I. et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res., 31, 365-370.
15. Greer,D.S., Westbrook,J.D. and Bourne,P.E. (2002) An ontology driven architecture for derived representations of macromolecular structure. Bioinformatics, 18, 1280-1281.