A systematic comparison of protein structure classifications: SCOP, CATH and FSSP

Structure

Volumn 7, Issue 9, 1999, Pages 1099-1112

  Hadley, Caroline ^a   Jones, David T ^a  

^a UNIVERSITY OF WARWICK   (United Kingdom)

Author keywords

Evolution; Protein folds; Protein structure classification; Taxonomy

Indexed keywords

ARTICLE; COMPARATIVE STUDY; DATA BASE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN STRUCTURE;

EID: 0033200307     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(99)80177-4     Document Type: Article

References (36)

1. 1. Bernstein, F.C., et al., & Tasumi, M. (1977). The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542.
2. 2. Richardson, J.S. (1981 ). The anatomy and taxonomy of protein structure. Adv. Protein Chem. 34, 167-339.
3. 3. Crippen, G.M. (1978). The tree structural organization of proteins. J. Mol. Biol. 126, 315-332.
4. 4. Rose, G.D. (1985). Automatic recognition of domains in globular proteins. Methods Enzymol. 115, 430-440.
5. 5. Wodak, S.J. & Janin, J. (1981). Location of structural domains in proteins. Biochemistry 20, 6544-6552.
6. 6. Holm, L. & Sander, C. (1994). Parser for protein folding units. Proteins 19, 256-268.
7. 7. Swindells, M.B. (1995). A procedure for detecting structural domains in proteins. Protein Sci. 4, 103-112.
8. 8. Levitt, M. & Chothia, C. (1976). Structural patterns in globular proteins. Nature 261, 552-558.
9. 9. Murzin, A.G., Brenner, S.E., Hubbard, T. & Chothia, C. (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.
10. 10. Orengo, C.A., Michie, A.D., Jones, S., Jones, D.T., Swindells, M.B. & Thornton, J.M. (1997). CATH-a hierarchic classification of protein domain structures. Structure 5, 1093-1108.
11. 11. Holm, L., Ouzounis, C., Sander, C., Tuparev, G. & Vriend, G. (1992). A database of protein structure families with common folding motifs. Protein Sci. 1, 1691-1698.
12. 12. Jones, S., Stewart, M., Michie, A., Swindells, M.B., Orengo, C.A. & Thornton, J.M. (1998). Domain assignment for protein structures using a consensus approach: characterization and analysis. Protein Sci. 7, 233-242.
13. 13. Michie, A.D., Orengo, C.A. & Thornton, J.M. (1996). Analysis of domain structural class using an automated class assignment protocol. J. Mol. Biol. 262, 168-185.
14. 14. Taylor, W.R. & Orengo, C.A. (1989). Protein structure alignment. J. Mol. Biol. 208, 1-22.
15. 15. Orengo, C.A., Brown, N.P. & Taylor, W.R. (1992). Fast structure alignment for protein databank searching. Proteins 14, 139-167.
16. 16. Holm, L. & Sander, C. (1994). The FSSP database of structurally aligned protein fold families. Nucleic Acids Res. 22, 3600-3609.
17. 17. Holm, L. & Sander, C. (1993). Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 123-138.
18. 18. Martin, A.C., et al., & Thornton, J. M. (1998). Protein folds and functions. Structure 6, 875-884.
19. 19. Abagyan, R.A. & Batalov, S. (1997). Do aligned sequences share the same fold? J. Mol. Biol. 273, 355-368.
20. 20. Russell, R.B., Saqi, M.A., Bates, P.A., Sayle, R.A. & Sternberg, M.J.E. (1998). Recognition of analogous and homologous protein folds-assessment of prediction success and associated alignment accuracy using empirical substitution matrices. Protein Eng. 11, 1-9.
21. 21. Murzin, A.G. & Bateman, A. (1997). Distant homology recognition using structural classification of proteins. Proteins 1, 105-112.
22. 22. Chou, K.C. & Maggiora, G.M. (1998). Domain structural class prediction. Protein Eng. 11, 523-538.
23. 23. Gerstein, M. & Levitt, M. (1998). Comprehensive assessment of automatic structural alignment against a manual standard, the SCOP classification of proteins. Protein Sci. 7, 445-456.
24. 24. Zhang, C.T. (1997). Relations of the numbers of protein sequences, families and folds. Protein Eng. 10, 757-761.
25. 25. Wang, Z.X. (1998). A re-estimation for the total numbers of protein folds and superfamilies. Protein Eng. 11, 621-626.
26. 26. Madej, T., Gibrat, J-F. & Bryant, S.H. (1995). Threading a database of protein cores. Proteins 23, 356-369.
27. 27. Gibrat, J-F., Madej, T. & Bryant, S.H. (1996). Surprising similarities in structure comparison. Curr. Opin. Struct. Biol. 6, 377-385.
28. 28. Mizuguchi, K., Deane, C.M., Blundell, T.L. & Overington, J.P. (1998). HOMSTRAD: a database of protein structure alignments for homologous families. Protein Sci. 7, 2469-2471.
29. 29. Sowdhamini, R., Rufino, S.D. & Blundell, T.L. (1996). A database of globular protein structural domains: clustering of representative family members into similar folds. Fold. Des. 1, 209-220.
30. 30. Siddiqui, A.S. & Barton, G.J. (1995). Continuous and discontinuous domains: an algorithm for the automatic generation of reliable protein domain definitions. Protein Sci. 4, 872-884.
31. 31. Chothia, C. (1992). Proteins: One thousand families for the molecular biologist. Nature 357, 543-544.
32. 32. Blundell, T.L. & Johnson, M.S. (1993). Catching a common fold. Protein Sci. 2, 877-883.
33. 33. Orengo, C.A., Jones, D.T. & Thornton, J.M. (1994). Protein superfamilies and domain superfolds. Nature 372, 631-634.
34. 34. Alexandrov, N.N. & Go, N. (1994). Biological meaning, statistical significance, and classification of local spatial similarities in nonhomologous proteins. Protein Sci. 3, 866-875.
35. 35. Sayle, R.A. & Milner-White, E.J. (1995). RASMOL: biomolecular graphics for all. Trends Biochem. Sci. 20, 374.
36. 36. Kraulis, P.J. (1991). MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946-950.