DomNet: Protein domain boundary prediction using enhanced general regression network and new profiles

IEEE Transactions on Nanobioscience

Volumn 7, Issue 2, 2008, Pages 172-181

  Yoo, Paul D ^a   Sikder, Abdur R ^b   Taheri, Javid ^a   Zhou, Bing Bing ^a   Zomaya, Albert Y ^a  

^a UNIVERSITY OF SYDNEY   (Australia)

^b MICHIGAN TECHNOLOGICAL UNIVERSITY   (United States)

Author keywords

Domain boundary prediction; Domain linker index; Machine learning; Sequence encoding; Sequence profile

Indexed keywords

ARCHITECTURAL DESIGN; ARTIFICIAL INTELLIGENCE; COMPUTER NETWORKS; CORRELATION METHODS; EDUCATION; FARM BUILDINGS; FOOD PROCESSING; FORECASTING; LEARNING ALGORITHMS; METROPOLITAN AREA NETWORKS; MULTITASKING; NETWORK PROTOCOLS; ROBOT LEARNING; STRUCTURAL DESIGN;

ART MODELS; BENCHMARK DATASET; CORRELATION COEFFICIENT (CC); DATA SETS; DOMAIN BOUNDARIES; EVOLUTION (CO); GENERAL (CO); INTER DOMAIN; MACHINE LEARNING TECHNIQUES; MACHINE-LEARNING; MULTIDOMAINS; PREDICTIVE PERFORMANCE; PROTEIN DOMAINS; PROTEIN STRUCTURES; REGRESSION (R2); SECONDARY STRUCTURES; SOLVENT ACCESSIBILITY; SUPERIOR PERFORMANCE; TARGET SEQUENCES;

LEARNING SYSTEMS;

ACCURACY; ARTICLE; CORRELATION COEFFICIENT; MACHINE LEARNING; PROTEIN DOMAIN; PROTEIN SECONDARY STRUCTURE; QUALITY CONTROL; SENSITIVITY AND SPECIFICITY;

AMINO ACID SEQUENCE; COMPUTER SIMULATION; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, TERTIARY; PROTEINS; REGRESSION ANALYSIS; SEQUENCE ANALYSIS, PROTEIN;

EID: 45249093424     PISSN: 15361241     EISSN: None     Source Type: Journal    
DOI: 10.1109/TNB.2008.2000747     Document Type: Article

References (54)

1. R. R. Copley, T. Doerksa, I. Letunica, and P. Borka, "Protein domain analysis in the era of complete genomes," FEBS Lett., vol. 513, pp. 129-134, 2002.
2. M. Levitt and C. Chothia, "Structural patterns in globular proteins," Nature, vol. 261, pp. 552-558, 1976.
3. J. S. Richardson, "The anatomy and taxonomy of protein structure," Adv. Protein CHem, vol. 34, pp. 167-339, 1981.
4. P. Bork, "Shuffled domains in extracellular proteins," FEBS Lett., vol. 286, pp. 47-54, 1991.
5. D. B. Wetlaufer, "Nucleation, rapid folding, and globular intrachain regions in proteins," Proc. Natl. Acad. Sci. USA, vol. 70, pp. 697-701, 1973.
6. C. Chothia, "Proteins. One thousand families for the molecular biologist," Nature, vol. 357, pp. 543-544, 1992.
7. M. Suyama and O. Ohara, "DomCut: Prediction of inter-domain linker regions in amino acid sequences," Bioinformatics, vol. 19, no. 5, pp. 673-674, 2003.
8. B. Contreras-Moreira and P. A. Bates, "Domain fishing: A first step in protein comparative modeling," Bioinformatics, vol. 18, pp. 1141-1142, 2002.
9. S. J. Wheelan, A. Marchler-Bauer, and S. H. Bryant, "Domain size distributions can predict domain boundaries," Bioinformatics, vol. 16, pp. 613-618, 2000.
10. J. Gracy and P. Argos, "DOMO: A new database of aligned protein domains," Trends Biochem. Sci., vol. 23, pp. 495-497, 1998.
11. S. Veretnik and I. N. Shindyalov, , Y. Xu, D. Xu, and J. Liang, Eds., Computational Methods for Domain Partitioning in Protein Structures in Computational Methods for Protein Structure and Modeling. New York: Springer-Verlag, 2006.
12. O. V. Galzitskaya and B. S. Melnik, "Prediction of protein domain boundaries from sequence alone," Protein Science, vol. 12, pp. 696-701, 2003.
13. J. Cheng, M. Sweredoski, and P. Baldi, "DOMpro: Protein domain prediction using profiles, secondary structure, relative solvent accessibility, and recursive neural networks," Data Mining Knowledge Discovery, vol. 13, no. 1, pp. 1-10, 2006.
14. J. Liu and B. Rost, "Sequence-based prediction of protein domains," Nucleic Acids Res., vol. 32, no. 12, pp. 3522-3530, 2004.
15. R. A. George and J. Heringa, "SnapDRAGON: A method to delineate protein structural domains from sequence data," J. Mol. Biol., vol. 316, pp. 839-851, 2002.
16. R. L. Marsden, L. J. McGuffin, and D. T. Jones, "Rapid protein domain assignment from amino acid sequence using predicted secondary structure," Protein Sci., vol. 11, pp. 2814-2824, 2002.
17. N. Nagarajan and G. Yona, "Automatic prediction of protein domains from sequence information using a hybrid learning system," Bioinformatics, vol. 20, pp. 1335-1360, 2004.
18. J. E. Gewehr and R. Zimmer, "SSEP-domain: Protein domain prediction by alignment of secondary structure elements and profiles," Bioinformatics, vol. 22, no. 2, pp. 181-187, 2006.
19. M. Dumontier, R. Feldman, H. J. Yao, and C. W. V. Hogue, "Armidillo: Doamin boundary prediction by amino acid composition," J. Mol. Biol., vol. 350, pp. 1061-1073, 2005.
20. M. Suyama and O. Ohara, "DomCut: Prediction of inter-domain linker regions in amino acid sequences," Bioinformatics, vol. 19, no. 5, pp. 673-674, 2003.
21. J. Sim, S.-Y. Kim, and J. Lee, "PRODO: Prediction of protein domain boundaries using neural networks," Proteins, vol. 59, pp. 627-632, 2005.
22. A. R. Sikder and A. Y. Zomaya, "Improving the performance of domain discovery of protein domain boundary assignment using inter-domain linker index," BMC Bioinformatics, vol. 7, p. S6, 2006.
23. R. R. Joshi, "A decade of computing to traverse the labyrinth of protein domains," Current Bioinformatics, vol. 2, pp. 113-131, 2007.
24. R. S. Gokhale and C. Khosla, "Role of linkers in communication between protein modules," Curr. Opin. Chem. Biol., vol. 4, pp. 22-27, 2000.
25. C. Civera, B. Simon, G. Stier, M. Sattler, and M. J. Macias, "Structure and dynamics of the human pleckstrin DEP domain: Distinct molecular features of a novel DEP domain subfamily," Proteins: Struct. Funct. Genet., vol. 58, pp. 354-366, 2005.
26. C. R. Robinson and R. T. Sauer, "Optimizing the stability of singlechain proteins by linker length and composition mutagenesis," Proc. Natl. Acad. Sci. USA, vol. 95, pp. 5929-5934, 1998.
27. H. C. van Leeuwen, M. J. Strating, M. Rensen, W. deLaat, and P. C. van der Vliet, "Linker length and composition influence the flexibility of Oct-1 DNA binding," EMBO J., vol. 16, pp. 2043-2053, 1997.
28. M. J. Lehtinen, S. Meri, and T. S. Jokiranta, "Inter-domain contact regions and angles between adjacent short consensus repeat domains," J. Mol. Biol., vol. 344, pp. 1385-1396, 2004.
29. T. A. Holland, S. Veretnik, I. N. Shindyalov, and P. E. Bourne, "Partitioning protein structures into domains: Why is it so difficult?," J. Mol. Biol., vol. 361, no. 3, pp. 562-590, 2006.
30. F. M. G. Pearl, D. Lee, J. E. Bray, I. Sillitoe, A. E. Todd, A. P. Harrison, J. M. Thornton, and C. A. Orengo, "Assigning genomic sequences to CATH," Nucleic Acids Res., vol. 28, no. 1, pp. 277-282, 2000.
31. A. Andreeva, D. Howorth, S. E. Brenner, T. J. Hubbard, C. Chothia, and A. G. Murzin, "SCOP database in 2004: Refinements integrate structure and sequence family data," Nucleic Acids Res., vol. 32, pp. D226-D229, 2004.
32. H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindylov, and P. E. Bourne, "The protein data bank," Nucleic Acids Res., vol. 28, pp. 235-242, 2000.
33. G. Pollastri, D. Przybylski, B. Rost, and P. Baldi, "Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles," Proteins, vol. 47, pp. 228-235, 2002.
34. G. Pollastri, P. Baldi, P. Fariselli, and R. Casadio, "Prediction of coordination number and relative solvent accessibility in proteins," Proteins, vol. 47, pp. 142-153, 2002.
35. S. F. Altschul, T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman, "Gapped BLAST and PSI-BLAST: A new generation of protein database search programs," Nucleic Acids Res., vol. 25, no. 17, pp. 3389-3402, 1997.
36. A. Marchler-Bauer et al., "CDD: A conserved domain database for protein classification," Nucleic Acids Res., vol. 33, pp. D192-D196, 2006.
37. A. Vieira and B. Oliva, "Protein loop classification using artificial neural networks," LNBI, vol. 3594, pp. 222-225, 2005.
38. W. Hardle, M. Muller, S. Sperlich, and A. Warwatz, Nonparametric and Semiparametric Models. New York: Springer, 2004.
39. J. C. B. Melo, G. D. C. Cavalcanti, and K. S. Guimaraes, "PCA feature extraction for protein structure prediction," in IEEE Proc. 2003 Int. Joint Conf. Neural Networks, OR, 2003.
40. P. D. Yoo, A. R. Sikder, B. B. Zhou, and A. Y. Zomaya, "Improved general regression network for domain boundary prediction," BMC Bioinfomatics, vol. 9, p. S12, 2008.
41. M. Kramer, "Nonlinear principal component analysis using autoassociative neural networks," AIChE J., vol. 37, pp. 233-243, 1991.
42. Y. Freund and R. E. Schapire, "Experiments with a new boosting algorithm," in Machine Learning: Proc. 13th Int. Conf., 1996, pp. 148-156.
43. R. E. Schapire, "A brief introduction to boosting," in Proc. 16th Int. Joint Conf. Artif. Intell., 1999, pp. 1401-1406.
44. J. Chen and N. S. Chaudhari, "Bidirectional segmented-memory recurrent neural network for protein secondary structure prediction," Soft Comput. J., vol. 10, pp. 315-324, 2005.
45. A. A. Ceroni and P. Frasconi, "On the role of long-range dependencies in learning protein secondary structure," IEEE Proc. Neural Networks, vol. 3, pp. 1899-1904, 2004.
46. D. Frishman and P. Argos, "Incorporation of non-local interactions in protein secondary structure prediction from the amino acid sequence," Protein Eng., vol. 9, pp. 133-142, 1996.
47. R. D. King and M. J. E. Sternberg, "Identification and application of the concepts important for accurate and reliable protein secondary structure prediction," Protein Sci., vol. 5, pp. 2298-2310, 1996.
48. B. Rost and C. Sander, "Prediction of protein secondary structure at better than 70% accuracy," J. Molecular Biol., vol. 232, pp. 584-599, 1993.
49. A. A. Salamov and V. V. Solovyev, "Prediction of protein secondary structure by combining nearest- neighbor algorithms and multiple sequence alignments," J. Molecular Biol., vol. 247, pp. 11-15, 1995.
50. M. J. Zvelebil, G. J. Barton, W. R. Taylor, and M. J. E. Sternberg, "Prediction of protein secondary structure and active sites using alignment of homologous sequence," J. Molecular Biol., vol. 194, pp. 957-961, 1987.
51. C. Notredame, "Recent progress in multiple sequence alignment: A survey," Phar-Macogenomics, vol. 3, pp. 131-144, 2002.
52. R. C. Edgar and S. Batzoglou, "Multiple sequence alignment," Current Opinion Structural Biol., vol. 16, pp. 368-373, 2006.
53. R. C. Edgar and K. Sjölander, "A comparison of scoring functions for protein sequence profile alignment," Bioinformatics, vol. 20, no. 8, pp. 1301-1308, 2004.
54. J. D. Thompson, F. Plewniak, and O. Poch, "A comprehensive comparison of multiple sequence alignment programs," Nucleic Acids Res., vol. 27, pp. 2682-2690, 1999.