E-MSD: The European Bioinformatics Institute macromolecular structure database

Nucleic Acids Research

Volumn 31, Issue 1, 2003, Pages 458-462

  Boutselakis, H ^a   Dimitropoulos, D ^a   Fillon, J ^a   Golovin, A ^a   Henrick, K ^a   Hussain, A ^a   Ionides, J ^a   John, M ^a   Keller, P A ^a   Krissinel, E ^a   McNeil, P ^a   Naim, A ^a   Newman, R ^a   Oldfield, T ^a   Pineda, J ^a   Rachedi, A ^a   Copeland, J ^a   Sitnov, A ^a   Sobhany, S ^a   Suarez Uruena, A ^a   Swaminathan, J ^a   Tagari, M ^a   Tate, J ^a   Tromm, S ^a   Velankar, S ^a   Vranken, W ^a   more..

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EUROPEAN BIOINFORMATICS INSTITUTE MACROMOLECULAR STRUCTURE DATABASE; GENE TECHNOLOGY; INTERNET; LIGAND BINDING; MACROMOLECULE; NUCLEIC ACID DATABASE; NUCLEIC ACID STRUCTURE; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN SECONDARY STRUCTURE; REVIEW;

ANIMALS; BINDING SITES; COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; DATABASES, PROTEIN; EUROPE; LIGANDS; PROTEIN STRUCTURE, SECONDARY; PROTEINS; REPRODUCIBILITY OF RESULTS; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 0037246807     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg065     Document Type: Review

References (34)

1. Hamm,G.H. and Cameron,G.N. (1986) The EMBL data library. Nucleic Acids Res., 14, 5-10.
2. Bairoch,A. and Boeckmann,B. (1994) The SWISS-PROT protein sequence databank: current status. Nucleic Acids Res., 22, 3578-3580.
3. Bairoch,A. and Apweiler,R. (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acid Res., 28, 45-48.
4. 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.
5. Service,R.F. (2000) Structural genomics offers high-speed look at proteins. Science, 287, 194-196.
6. Dubois,P. (1999) MySQL. New Riders Press, ISBN 0735709211.
7. Henrick,K. and Thornton,J.M. (1998) PQS: a Protein Quarternary File Server. Trends Biochem. Sci., 23, 358-361.
8. Lin,D., Manning,N.O., Jiang,J.S., Abola,E.E., Stampf,D., Prilusky,J. and Sussman,J.L. (2000) Autodep: a web based system for deposition and validation of macromolecular structural information. Acta Crystallogr., D56, 828-841.
9. Ponstingl,H., Henrick,K. and Thornton,J.M. (2000) Discriminating between homodimeric and monomeric proteins in the crystalline state. Proteins, 41, 47-57.
10. Apweiler,R., Attwood,T.K., Bairoch,A., Bateman,A., Birney,E., Biswas,M., Bucher,P., Cerutti,L., Corpet,F., Croning,M.D.R., Durbin,R., Falquet,L., Fleischmann,W., Gouzy,J., Hermjakob,H., Hulo,N., Jonassen,I., Kahn,D., Kanapin,A., Karavidopoulou,Y., Lopez,R., Marx,B., Mulder,N.J., Oinn,T.M., Pagni,M., Servant,F., Sigrist,C.J.A. and Zdobnov,E.M. (2001) InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res., 29, 37-40.
11. The Gene Ontology Consortium (2001) Creating the gene ontology resource: design and implementation. Genome Res., 11, 1425-1433.
12. Murzin,A.G., Brenner,S.E., Hubbard,T. and Chothia,C. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
13. Orengo,C.A., Michie,A.D., Jones,S., Jones,D.T., Swindells,M.B. and Thornton,J.M. (1997) CATH-a hierarchic classification of protein domain structures. Structure, 5, 1093-1108.
14. Bateman,A., Birney,E., Cerruti,L., Durbin,R., Etwiller,L., Eddy,S.R., Griffiths-Jones,S., Howe,K.L., Marshall,M. and Sonnhammer,E.L. (2002) The Pfam families database. Nucleic Acids Res., 30, 276-280.
15. Hofmann,K., Bucher,P., Falquet,L. and Bairoch,A. (1999) The PROSITE database, its status in 1999. Nucleic Acids Res., 27, 215-219.
16. Kabsch,W. and Sander,C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
17. Hutchinson,E.G. and Thornton,J.M. (1996) PROMOTIF-a program to identify and analyze structural motifs in proteins. Protein Sci., 5, 212-220.
18. Weininger,D., Weininger,A. and Weininger,J.L. (1989) SMILES2 algorithm for generation of unique smiles notation. J. Chem. Inf. Comput. Sci, 29, 97-101. For a more recent exposition on the SMILES language, see Daylight Theory Manual, Chapter 3, Daylight Chemical Information Systems, Inc., 18500 Von Karman Ave. 450, Irvine, CA 92715, USA.
19. Pedretti,A., Villa,L. and Vistoli,G. (2002) VEGA: a versatile program to convert, handle and vusualize molecular structure on winows-based PCs. J. Mol. Graph., 21, 47-49.
20. Sadowski,J., Gasteiger,J. and Klebe,G. (1994) Comparison of automatic three-dimensional model builders using 639 X-Ray structures. J. Chem. Inf. Comput. Sci., 34, 1000-1008.
21. Ihlenfeldt,W.D., Takahashi,Y., Abe,H. and Sasaki,S. (1994) Computation and Management of Chemical Properties in CACTVS: An extensible Networked Approach toward Modularity and Flexibility. J. Chem. Inf. Comput. Sci., 34, 109-116.
22. Ullman,J.R. (1976) An algorithm for subgraph isomorphism. J. Assoc. Comput. Mach., 23, 31-42.
23. Krissinel,E., Velankar,S. and Henrick,K. (in press). Protein Structure comparison based on a new algorithm for common subgraph isomorphism.
24. Brunger,A.T., Adams,P.D., Clore,G.M., Delano,W.L., Gros,P., Grosse-Kunstleve,R.W., Jiang,J.-S., Kuszewski,J., Nilges,M., Pannu,N.S., Read,R.J., Rice,L.M., Simonson,T. and Warren,G.L. (1998) Crystallography and NMR System. Acta Crystallogr., D54, 905-921.
25. Collaborative Computational Project, Number 4 (1994) The CCP4 Suite Programs for Protein Crystallography. Acta Cryst., D50, 760-763.
26. See also Murshudov,G.N., Vagin,A.A. and Dodson,E.J. (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr., D53, 240-255.
27. Ertl,P. and Jacob,O. (1997) WWW-based Chemical Information System. Theochem, 419, 113-120.
28. Bourne,P., 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.
29. Bernstein,H.J. (2000) Recent changes to RasMol, recombining the variants. Trends Biochem. Sci., 25, 453-455;
30. Sayle,R. and Milner-White,E.J. (1995) RasMol: biomolecular graphics for all. Trends Biochem. Sci., 20, 374.
31. National Library of Medicine (1989) MEDLINE [database online]. Bethesda (MD). Updated weekly. Available from: National Library of Medicine; OVID, Murray, UT; The Dialog Corporation, Palo Alto, CA.
32. Wheeler,D.L., Chappey,C., Lash,A.E., Leipe,D.D., Madden,T.L., Schuler,G.D., Tatusova,T.A. and Rapp,B.A. (2000) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 28, 10-14.
33. Holm,L. and Sander,C. (1999) Protein folds and families: sequence and structure alignments. Nucleic Acids Res., 27, 244-247.
34. Schomburg,I., Chang,A. and Schomburg,D. (2002) BRENDA, enzyme data and metabolic information. Nucleic Acids Res., 30, 147-149.