A consensus view of fold space: Combining SCOP, CATH, and the Dali Domain Dictionary

Protein Science

Volumn 12, Issue 10, 2003, Pages 2150-2160

  Day, Ryan ^a   Beck, David A C ^a   Armen, Roger S ^a   Daggett, Valerie ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

CATH; Dali; Fold classification; SCOP

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; CLASSIFICATION; INTERMETHOD COMPARISON; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN STRUCTURE; PROTEIN SYNTHESIS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

AMINO ACID MOTIFS; COMPUTATIONAL BIOLOGY; COMPUTER GRAPHICS; DATABASES, PROTEIN; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; PROTEINS; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 0141524060     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.0306803     Document Type: Article

References (24)

1. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., and Bourne, P.E. 2000a. The Protein Data Bank. Nucleic Acids Res. 28: 235-242.
2. Berman, H.M., Bhat, T.N., Bourne, P.E., Feng, Z., Gilliland, G., Wiessig, H., and Westbrook, J. 2000b. The Protein Data Bank and the challenge of structural genomics. Nat. Struct. Biol. 7: 957-959.
3. Brenner, S.E., Koehl, P., and Levitt, M. 2000. The ASTRAL compendium for sequence and structure analysis. Nucleic Acids Res. 28: 254-256.
4. Chandonia, J.M., Walker, N.S., Lo Conte, L., Koehl, P., Levitt, M., and Brenner, S.E. 2002. ASTRAL compendium enhancements. Nucleic Acids Res. 30: 260-263.
5. Dengler, U., Siddiqui, A.S., and Barton, G.J. 2001. Protein structural domains: Analysis of the 3Dee domains database. Proteins 42: 332-344.
6. Dietmann, S. and Holm, L. 2001. Identification of homology in protein structure classification. Nat. Struct. Biol. 8: 953-957.
7. Dietmann, S., Park, J., Notredame, C., Heger, A., Lappe, M., and Holm, L. 2001. A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3. Nucleic Acids Res. 29: 55-57.
8. Eidhammer, I., Jonassen, I., and Taylor, W.R. 2000. Structure comparison and structure patterns. J. Comp. Biol. 7: 685-716.
9. Ferrin, T.E., Huang, C.C., Jarvis, L.E., and Langridge, R. 1988. The MIDAS display system. J. Mol. Graphics 6: 13-27.
10. Gerstein, M. and Levitt, M. 1998. Comprehensive assessment of automatic structural alignment against a manual standard, the SCOP classification of proteins. Protein Sci. 7: 445-456.
11. Getz, G., Vendruscolo, M., Sachs, D., and Domany, E. 2002. Automated assignment of SCOP and CATH protein structure classifications from FSSP scores. Proteins 46: 405-415.
12. Hadley, C. and Jones, D.T. 1999. A systematic comparison of protein structure classifications: SCOP, CATH, and FSSP. Structure 7: 1099-1112.
13. Holm, L. and Sander, C. 1994. Parser for protein folding units. Proteins 19: 256-268.
14. -. 1998. Dictionary of recurrent domains in protein structures. Proteins 33: 88-96.
15. Jones, S., Stewart, M., Michie, A., Swindells, M.B., Orengo, C., and Thornton, J.M. 1998. Domain assignment for protein structures using a consensus approach: Characterization and analysis. Protein Sci. 7: 233-242.
16. May, A.C.W. 1999. Toward more meaningful hierarchical classification of protein three-dimensional structures. Proteins 37: 20-29.
17. McGuffin, L.J., Bryson, K., and Jones, D.T. 2001. What are the baselines of protein fold recognition? Bioinformatics 17: 63-72.
18. 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.
19. Orengo, C.A. 1999. CORA - Topological fingerprints for protein structural families. Protein Sci. 8: 699-715.
20. 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.
21. Sauder, J.M., Arthur, J.W., and Dunbrack, R.L. 2000. Large-scale comparison of protein sequence alignment algorithms with structure alignments. Proteins 40: 6-22.
22. Shindyalov, I.N. and Bourne, P.E. 2000. An alternative view of protein fold space. Proteins 38: 247-260.
23. Taylor, W.R. and Orengo, C.A. 1989. Protein structure alignment. J Mol. Biol. 208: 1-22.
24. Westhead, D.R., Slidel, T.W.F., Flores, T.P.J., and Thornton, J.M. 1999. Protein structural topology: Automated analysis and diagrammatic representation. Protein Sci. 8: 897-904.