Fold recognition via a tree

Journal of Computational Biology

Volumn 13, Issue 9, 2006, Pages 1565-1573

  Chen, Yu ^a   Crippen, Gordon M ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

Multiple alignment; Protein structure classification

Indexed keywords

ALGORITHM; ANALYTIC METHOD; ARTICLE; CLASSIFICATION; MATHEMATICAL ANALYSIS; METHODOLOGY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN STRUCTURE; SAUCE METHOD; SEQUENCE HOMOLOGY; STRUCTURAL PROTEOMICS; STRUCTURE ANALYSIS; TECHNIQUE;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; BIOMETRY; DATABASES, PROTEIN; MODELS, MOLECULAR; MODELS, STATISTICAL; PROTEIN FOLDING; PROTEINS; PROTEOMICS; SEQUENCE ALIGNMENT;

EID: 33845364564     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2006.13.1565     Document Type: Article

References (19)

1. Altschul, S.F., Madden, T.L., Schaffer, A.A., et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
2. Bowie, J.U., Luthy, R., and Eisenberg, D. 1991. A method to identify protein sequences that fold into a known three-dimensional structure. Science 253, 164-170.
3. Chen, Y., and Crippen, G.M. 2005. A novel approach to structural alignment using realistic structural and environmental information. Protein Sci. 14, 2935-2946.
4. Chen, Y., and Crippen, G.M. 2006. An iterative refinement algorithm for consistency based multiple structural alignment methods. Bioinformatics 22, 2087-2093.
5. Ding, C.H.Q., and Dubchak, I. 2001. Multi-class protein fold recognition using support vector machines and neural networks. Bioinformatics 17, 349-358.
6. Han, S., Lee, B., Yu, S., et al. 2005. Fold recognition by combining profile-profile alignment and support vector machine. Bioinformatics 21, 2667-2673.
7. Holm, L., and Sander, C. 1996. Mapping the protein universe. Science 273, 595-603.
8. Jones, D.T. 1999. GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J. Mol. Biol. 287, 797-815.
9. Kelley, L.A., MacCallum, R.M., and Sternberg, M.J.E. 2000. Enhanced genome annotation using structural profiles in the program 3D-PSSM. J. Mol. Biol. 299, 499-520.
10. Mallick, P., Weiss, R., and Eisenberg, D. 2002. The directional atomic solvation energy: an atom-based potential for the assignment of protein sequences to known folds. Proc. Natl. Acad. Sci. USA 99, 16041-16046.
11. Mizuguchi, K., Blundell, T.L., Gweon, H.S., et al. 2005. Homology recognition using environment-specific substitution scores enriched with homologous sequence information. Available at: www.forcasp.org/paper1760.html. Accessed September 13, 2006.
12. Murzin, A.G., Brenner, S.E., Hubbard, T., et al. 2005. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.
13. Norvell, J.C., and Machalek, A.Z. 2000. Structural genomics programs at the U.S. National Institute of General Medical Sciences. Nat. Struct. Biol. S7, 931.
14. Notredame, C., Higgins, D.G., and Heringa, J. 2000. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302, 205-217.
15. Orengo, C.A., Michie, A.D., Jones, S., et al. 1997. CATH-a hierarchic classification of protein domain structures. Structure 5, 1093-1108.
16. R Development Core Team. 2005. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. Available at: www.R-project.org. Accessed September 13, 2006.
17. Shi, J., Blundell, T.L., and Mizuguchi, K. 2001. FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J. Mol. Biol. 310, 243-257.
18. Xu, J., Li, M., Kim, D., et al. 2003. RAPTOR: optimal protein threading by linear programming. J. Bioinform. Comput. Biol. 1, 95-117.
19. Zhou, H., and Zhou, Y. 2005. Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments. Proteins 58, 321-328.