Improving the performance of DomainParser for structural domain partition using neural network

Nucleic Acids Research

Volumn 31, Issue 3, 2003, Pages 944-952

  Guo, Jun Tao ^a   Xu, Dong ^a   Kim, Dongsup ^a   Xu, Ying ^a,b  

^a Informatics Group   (United States)

^b OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; ARTIFICIAL NEURAL NETWORK; COMPUTER PROGRAM; CONTROLLED STUDY; DATA BASE; DECOMPOSITION; HYDROPHOBICITY; MOLECULAR EVOLUTION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STRUCTURE; REVIEW;

ALGORITHMS; ANIMALS; BETA-CRYSTALLIN B CHAIN; HYDROPHOBICITY; MODELS, MOLECULAR; NEURAL NETWORKS (COMPUTER); PROTEIN STRUCTURE, TERTIARY; PROTEINS;

EID: 0037324306     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg189     Document Type: Review

References (27)

1. Wetlaufer,D.B. (1973) Nucleation, rapid folding and globular intrachain regions in proteins. Proc. Natl Acad. Sci. USA, 70, 697-701.
2. Richardson,J.S. (1981) The anatomy and taxonomy of protein structure. Adv. Protein Chem., 34, 167-339.
3. 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.
4. 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.
5. Jones,D.T. (1999) GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J. Mol. Biol., 287, 797-815.
6. Kelley,L.A., MacCallum,R.M. and Sternberg,M.J. (2000) Enhanced genome annotation using structural profiles in the program 3D-PSSM. J. Mol. Biol., 299, 499-520.
7. Xu,Y. and Xu,D. (2000) Protein threading using PROSPECT: design and evaluation. Proteins, 40, 343-354.
8. National Institute of General Medical Sciences (1999) Pilot Projects for the Protein Structure Initiative (Structural Genomics). National Institute of General Medical Sciences, Bethesda, MD.
9. Holm,L. and Sander,C. (1994) Parser for protein folding units. Proteins, 19, 256-268.
10. Siddiqui,A.S. and Barton,G.J. (1995) Continuous and discontinuous domains: an algorithm for the automatic generation of reliable protein domain definitions. Protein Sci., 4, 872-884.
11. Swindells,M.B. (1995) A procedure for detecting structural domains in proteins. Protein Sci., 4, 103-112.
12. Wernisch,L., Hunting,M. and Wodak,S.J. (1999) Identification of structural domains in proteins by a graph heuristic. Proteins, 35, 338-352.
13. Xu,Y., Xu,D. and Gabow,H.N. (2000) Protein domain decomposition using a graph-theoretic approach. Bioinformatics, 16, 1091-1104.
14. 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.
15. Islam,S.A., Luo,J. and Sternberg,M.J. (1995) Identification and analysis of domains in proteins. Protein Eng., 8, 513-525.
16. Ford,L.R. and Fulkerson,D.R. (1962) Flows in Networks. Princeton University Press, Princeton, NJ.
17. Eisenberg,D., Weiss,R.M. and Terwilliger,T.C. (1982) The helical hydrophobic moment: a measure of the amphiphilicity of a helix. Nature, 299, 371-374.
18. Silverman,B.D. (2001) Hydrophobic moments of protein structures: spatially profiling the distribution. Proc. Natl Acad. Sci. USA, 98, 4996-5001.
19. Picard,J.C. and Queyranne,M. (1980) On the structure of all minimum cuts in a network and applications. Math. Programming Study, 13, 8-16.
20. Eisenberg,D., Weiss,R., Terwilliger,T. and Wilcox,W. (1982) Hydrophobic moments and protein structure. Faraday Symp. Chem. Soc., 17, 109-120.
21. Holm,L. and Sander,C. (1998) Dictionary of recurrent domains in protein structures. Proteins, 33, 88-96.
22. Wheelan,S.J., Marchler-Bauer,A. and Bryant,S.H. (2000) Domain size distributions can predict domain boundaries. Bioinformatics, 16, 613-618.
23. Riedmiller,M. and Braun,H. (1993) A direct adaptive method for faster backpropagation learning: the RPROP algorithm. In Proceedings of the International Conference on Neural Networks. IEEE, San Francisco, CA, pp. 586-591.
24. Hobohm,U., Scharf,M., Schneider,R. and Sander,C. (1992) Selection of representative protein data sets. Protein Sci., 1, 409-417.
25. Bernstein,F.C., Koetzle,T.F., Williams,G.J., Meyer,E.E.,Jr, Brice,M.D., Rodgers,J.R., Kennard,O., Shimanouchi,T. and Tasumi,M. (1977) The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol., 112, 535-542.
26. Taylor,W.R. (1999) Protein structural domain identification. Protein Eng., 12, 203-216.
27. Lo Conte,L., Brenner,S.E., Hubbard,T.J., Chothia,C. and Murzin,A.G. (2002) SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Res., 30, 264-267.