Relationship between global structural parameters and Enzyme Commission hierarchy: Implications for function prediction

Computational Biology and Chemistry

Volumn 40, Issue , 2012, Pages 15-19

  Boareto, Marcelo ^a   Yamagishi, Michel E B ^b   Caticha, Nestor ^a   Leite, Vitor B P ^c  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

^b EMBRAPA INFORMÁTICA AGROPECUÁRIA   (Brazil)

^c SÃO PAULO STATE UNIVERSITY UNESP   (Brazil)

Author keywords

Bioinformatics; EC hierarchy; Enzyme structure; Function prediction; Physicochemical parameters

Indexed keywords

ACTIVE SITE; CLASSIFICATION SYSTEM; DATA SETS; DISTANCE DISTRIBUTIONS; EC HIERARCHY; ENZYMATIC FUNCTIONS; ENZYME COMMISSIONS; ENZYME STRUCTURES; ESSENTIAL AMINO ACIDS; FUNCTION PREDICTION; GLOBAL STRUCTURE; HIERARCHICAL LEVEL; METRIC TENSOR; PHYSICOCHEMICAL CHARACTERISTICS; PHYSICOCHEMICAL PARAMETERS; PROTEIN DATABASE; PROTEIN MOTIFS; SEQUENCE ALIGNMENTS; STRUCTURAL PARAMETER; UNSUPERVISED CLUSTERING METHODS;

AMINO ACIDS; BIOINFORMATICS; CLUSTER ANALYSIS; FORECASTING; PROTEINS;

ENZYMES;

AMINO ACID; ENZYME; SOLVENT;

ARTICLE; BIOLOGY; CHEMICAL PHENOMENA; CHEMISTRY; ENZYME ACTIVE SITE; METABOLISM; PROTEIN CONFORMATION; PROTEIN DATABASE; SURFACE PROPERTY; TEMPERATURE;

AMINO ACIDS; CATALYTIC DOMAIN; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; ENZYMES; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; PROTEIN CONFORMATION; SOLVENTS; SURFACE PROPERTIES; TEMPERATURE;

EID: 84865326143     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2012.06.003     Document Type: Article

References (31)

1. G. Amitai, A. Shemesh, E. Sitbon, M. Shklar, D. Netanely, and I. Venger Network analysis of protein structures identifies functional residues Journal of Molecular Biology 344 4 2004 1135 1146
2. C. Berezin, F. Glaser, J. Rosenberg, I. Paz, T. Pupko, and P. Fariselli ConSeq: the identification of functionally and structurally important residues in protein sequences Bioinformatics 20 8 2004 1322 1324
3. M. Blatt, S. Wiseman, and E. Domany Superparamagnetic clustering of data Physical Review Letters 76 18 1996 3251 3254
4. T. Bojer, B. Hammer, D. Schunk, and K.T. von Toschanowitz Relevance determination in learning vector quantization Proc. of European Symposium on Artificial Neural Networks 2001
5. L.C. Borro, S.R.M. Oliveira, M.E.B. Yamagishi, A.L. Mancini, J.G. Jardine, and I. Mazoni Predicting enzyme class from protein structure using Bayesian classification Genetics and Molecular Research 5 1 2006 193 202
6. T. Bray, P. Chan, S. Bougouffa, R. Greaves, A.J. Doig, and J. Warwicker SitesIdentify: a protein functional site prediction tool BMC Bioinformatics 10 2009 379
7. T. Bray, A.J. Doig, and J. Warwicker Sequence and structural features of enzymes and their active sites by EC class Journal of Molecular Biology 386 5 2009 1423 1436
8. M. Brylinski, K. Prymula, W. Jurkowski, M. Kochanczyk, E. Stawowczyk, and L. Konieczny Prediction of functional sites based on the fuzzy oil drop model PLoS Computational Biology 3 5 2007 909 923
9. J.D. Bryngelson, and P.G. Wolynes Spin glasses and the statistical mechanics of protein folding Proceedings of the National Academy of Sciences of the United States of America 84 21 1987 7524 7528
10. Y.D. Cai, and K.C. Chou Using functional domain composition to predict enzyme family classes Journal of Proteome Research 4 1 2005 109 111
11. Y.D. Cai, G.P. Zhou, and K.C. Chou Predicting enzyme family classes by hybridizing gene product composition and pseudo-amino acid composition Journal of Theoretical Biology 234 1 2005 145 149
12. J.A. Capra, and M. Singh Predicting functionally important residues from sequence conservation Bioinformatics 23 15 2007 1875 1882
13. P.D. Dobson, and A.J. Doig Predicting enzyme class from protein structure without alignments Journal of Molecular Biology 345 1 2005 187 199
14. A.K. Dunker, I. Silman, V.N. Uversky, and J.L. Sussman Function and structure of inherently disordered proteins Current Opinion in Structural Biology 18 2008 756 764
15. D.U. Ferreiro, J.A. Hegler, E.A. Komives, and P.G. Wolynes Localizing frustration in native proteins and protein assemblies Proceedings of the National Academy of Sciences of the United States of America 104 50 2007 19819 19824
16. M.Y. Galperin, D.R. Walker, and E.V. Koonin Analogous enzymes: independent inventions in enzyme evolution Genome Research 8 8 1998 779 790
17. P.F. Gherardini, M.N. Wass, M. Helmer-Citterich, and M.J.E. Sternberg Convergent evolution of enzyme active sites is not a rare phenomenon Journal of Molecular Biology 372 3 2007 817 845
18. R.A. Goldstein, Z.A. Luthey-Schulten, and P.G. Wolynes Optimal protein-folding codes from spin-glass theory Proceedings of the National Academy of Sciences of the United States of America 89 11 1992 4918 4922
19. W.L. Huang, H.M. Chen, S.F. Hwang, and S.Y. Ho Accurate prediction of enzyme subfamily class using an adaptive fuzzy k-nearest neighbor method Biosystems 90 2 2007 405 413
20. R.A. Laskowski, J.D. Watson, and J.M. Thornton ProFunc: a server for predicting protein function from 3D structure Nucleic Acids Research 33 2005 W89 W93
21. A. Lobley, M.B. Swindells, C.A. Orengo, and D.T. Jones Inferring function using patterns of native disorder in proteins PLoS Computational Biology 3 2007 e162
22. A.C. Martin, C.A. Orengo, E.G. Hutchinson, S. Jones, M. Karmirantzou, and R.A. Laskowski Protein folds and functions Structure 6 7 1998 875 884
23. E. Nasibov, and C. Kandemir-Cavas Efficiency analysis of KNN and minimum distance-based classifiers in enzyme family prediction Computational Biology and Chemistry 33 6 2009 461 464
24. G. Neshich, R.C. Togawa, A.L. Mancini, P.R. Kuser, M.E.B. Yamagishi, and G. Pappas STING Millennium: a web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence Nucleic Acids Research 31 13 2003 3386 3392
25. J.N. Onuchic, and P.G. Wolynes Theory of protein folding Current Opinion in Structural Biology 14 1 2004 70 75
26. J.N. Onuchic, Z. Luthey-Schulten, and P.G. Wolynes Theory of protein folding: the energy landscape perspective Annual Review of Physical Chemistry 48 1 1997 545 600
27. C.A. Orengo, T.P. Flores, D.T. Jones, W.R. Taylor, and J.M. Thornton Recurring structural motifs in proteins with different functions Current Biology 3 3 1993 131 139
28. B. Rost Enzyme function less conserved than anticipated Journal of Molecular Biology 318 2 2002 595 608
29. M.I. Sadowski, and D.T. Jones The sequence-structure relationship and protein function prediction Current Opinion in Structural Biology 2009 357 362
30. Scop database. 2008. URL http://www.ebi.ac.uk.
31. E.C. Webb Enzyme nomenclature: recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzymes 1992 Academic Press New York