Predicting protein structural class based on multi-features fusion

Journal of Theoretical Biology

Volumn 253, Issue 2, 2008, Pages 388-392

  Chen, Chao ^a,b   Chen, Li Xuan ^c   Zou, Xiao Yong ^b   Cai, Pei Xiang ^b  

^a GUANGDONG PHARMACEUTICAL UNIVERSITY   (China)

^b SUN YAT SEN UNIVERSITY   (China)

^c Guangzhou Institute of Standardization   (China)

Author keywords

Fusion; Prediction; PROFEAT; Protein structural classes; Support vector machine

Indexed keywords

CELLULAR AUTOMATON; ENZYME; MEMBRANE; PHYSICOCHEMICAL PROPERTY; PREDICTION; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; JACKKNIFE TEST; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN STRUCTURE; STATISTICAL MODEL; SUPPORT VECTOR MACHINE;

AMINO ACID SEQUENCE; ANIMALS; CHEMISTRY, PHYSICAL; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; INTERNET; MODELS, STATISTICAL; PROTEIN CONFORMATION; PROTEINS; SEQUENCE ANALYSIS, PROTEIN;

EID: 45649085013     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2008.03.009     Document Type: Article

References (70)

1. Bahar I., Atilgan A.R., Jernigan R.L., and Erman B. Understanding the recognition of protein structural classes by amino acid composition. Proteins: Struct. Funct. Genet. 29 (1997) 172-185
2. Cai Y.D., and Chou K.C. Predicting enzyme subclass by functional domain composition and pseudo amino acid composition. J. Proteome Res. 4 (2005) 967-971
3. Cai Y.D., and Chou K.C. Using functional domain composition to predict enzyme family classes. J. Proteome Res. 4 (2005) 109-111
4. Cai Y.D., and Chou K.C. Predicting membrane protein type by functional domain composition and pseudo-amino acid composition. J. Theor. Biol. 238 (2006) 395-400
5. Cai Y.D., and Zhou G.P. Prediction of protein structural classes by neural network. Biochimie 82 (2000) 783-785
6. Cai Y.D., Liu X.J., Yu X.b., and Zhou G.P. Support vector machines for predicting protein structural class. BMC Bioinform. 2 (2001) 1-5
7. Cai Y.D., Liu X.J., Xu X.B., and Chou K.C. Prediction of protein structural classes by support vector machines. Comput. Chem. 26 (2002) 293-296
8. Cai Y.D., Feng K.Y., Lu W.C., and Chou K.C. Using LogitBoost classifier to predict protein structural classes. J. Theor. Biol. 238 (2006) 172-176
9. Cao Y.F., Liu S., Zhang L.D., Qin J., Wang J., and Tang K.X. Prediction of protein structural class with Rough Sets. BMC Bioinform. 7 (2006) 20-25
10. Chang, C.C., Lin, C.J., 2001. LIBSVM: A Library for Support Vector Machines. Software available at: 〈http://www.csie.ntu.edu.tw/~cjlin/libsvm〉.
11. Chen Y.L., and Li Q.Z. Prediction of apoptosis protein subcellular location using improved hybrid approach and pseudo-amino acid composition. J. Theor. Biol. 248 (2007) 377-381
12. Chen C., Tian Y.X., Zou X.Y., Cai P.X., and Mo J.Y. Using pseudo-amino acid composition and support vector machine to predict protein structural class. J. Theor. Biol. 243 (2006) 444-448
13. Chen C., Zhou X.B., Tian Y.X., Zou X.Y., and Cai P.X. Predicting protein structural class with pseudo-amino acid composition and support vector machine fusion network. Anal. Biochem. 357 (2006) 116-121
14. Chou K.C. A novel-approach to predicting protein structural classes in A (20-1)-d amino-acid-composition space. Proteins: Struct. Funct. Genet. 21 (1995) 319-344
15. Chou K.C. A key driving force in determination of protein structural classes. Biochem. Biophys. Res. Commun. 264 (1999) 216-224
16. Chou K.C. Using pair-coupled amino acid composition to predict protein secondary structure content. J. Protein Chem. 18 (1999) 473-480
17. Chou K.C. Prediction of protein structural classes and subcellular locations. Curr. Protein Peptide Sci. 1 (2000) 171-208
18. Chou K.C. Prediction of protein subcellular locations by incorporating quasi-sequence-order effect. Biochem. Biophys. Res. Commun. 278 (2000) 477-483
19. Chou K.C. Prediction of protein cellular attributes using pseudo-amino acid composition. Proteins: Struct. Funct. Genet. 43 (2001) 246-255
20. Chou K.C. Progress in protein structural class prediction and its impact to bioinformatics and proteomics. Curr. Protein Peptide Sci. 6 (2005) 423-436
21. Chou K.C. Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes. Bioinformatics 21 (2005) 10-19
22. Chou K.C., and Cai Y.D. Predicting protein structural class by functional domain composition. Biochem. Biophys. Res. Commun. 321 (2004) 1007-1009
23. Chou K.C., and Shen H.B. Predicting protein subcellular location by fusing multiple classifiers. J. Cell. Biochem. 99 (2006) 517-527
24. Chou K.C., and Zhang C.T. A correlation-coefficient method to predicting protein-structural classes from amino-acid compositions. Eur. J. Biochem. 207 (1992) 429-433
25. Chou K.C., and Zhang C.T. Predicting protein-folding types by distance functions that make allowances for amino-acid interactions. J. Biol. Chem. 269 (1994) 22014-22020
26. Chou K.C., and Zhang C.T. Prediction of protein structural classes. Crit. Rev. Biochem. Mol. Biol. 30 (1995) 275-349
27. Cortes C., and Vapnik V. Support-vector networks. Mach. Learn. 20 (1995) 273-297
28. Diao Y., Li M., Feng Z., Yin J., and Pan Y. The community structure of human cellular signaling network. J. Theor. Biol. 247 (2007) 608-615
29. Ding Y.S., Zhang T.L., and Chou K.C. Prediction of protein structure classes with pseudo amino acid composition and fuzzy support vector machine network. Protein Peptide Lett. 14 (2007) 811-815
30. Du P.F., and Li Y.D. Prediction of protein submitochondria locations by hybridizing pseudo-amino acid composition with various physicochemical features of segmented sequence. BMC Bioinform. 7 (2006) 518-525
31. Du Q.S., Wei D.Q., and Chou K.C. Correlations of amino acids in proteins. Peptides 24 (2003) 1863-1869
32. Du Q.S., Jiang Z.Q., He W.Z., Li D.P., and Chou K.C. Amino acid principal component analysis (AAPCA) and its applications in protein structural class prediction. J. Biomol. Struct. Dyn. 23 (2006) 635-640
33. Gao Q.B., and Wang Z.Z. Classification of G-protein coupled receptors at four levels. Protein Eng. Des. Sel. 19 (2006) 511-516
34. Gao Y., Shao S., Xiao X., Ding Y., Huang Y., Huang Z., and Chou K.C. Using pseudo amino acid composition to predict protein subcellular location: approached with Lyapunov index, Bessel function, and Chebyshev filter. Amino Acids 28 (2005) 373-376
35. Jahandideh S., Abdolmaleki P., Jahandideh M., and Asadabadi E.B. Novel two-stage hybrid neural discriminant model for predicting proteins structural classes. Biophys. Chem. 128 (2007) 87-93
36. Kedarisetti K.D., Kurgan L., and Dick S. Classifier ensembles for protein structural class prediction with varying homology. Biochem. Biophys. Res. Commun. 348 (2006) 981-988
37. Kohavi R., and John G.H. Wrappers for feature subset selection. Artif. Intell. 97 (1997) 273-324
38. Kurgan L.A., Stach W., and Ruan J. Novel scales based on hydrophobicity indices for secondary protein structure. J. Theor. Biol. 248 (2007) 354-366
39. Levitt M., and Chothia C. Structural patterns in globular proteins. Nature 261 (1976) 552-558
40. Li Z.R., Lin H.H., Han L.Y., Jiang L., Chen X., and Chen Y.Z. PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence. Nucleic Acids Res. 34 (2006) W32-W37
41. Lin H., and Li Q.Z. Predicting conotoxin superfamily and family by using pseudo amino acid composition and modified Mahalanobis discriminant. Biochem. Biophys. Res. Commun. 354 (2007) 548-551
42. Lin H., and Li Q.Z. Using pseudo amino acid composition to predict protein structural class: approached by incorporating 400 dipeptide components. J. Comput. Chem. 28 (2007) 1463-1466
43. Luo R.Y., Feng Z.P., and Liu J.K. Prediction of protein structural class by amino acid and polypeptide composition. Eur. J. Biochem. 269 (2002) 4219-4225
44. Mondal S., Bhavna R., Babu R.M., and Ramakumar S. Pseudo amino acid composition and multi-class support vector machines approach for conotoxin superfamily classification. J. Theor. Biol. 243 (2006) 252-260
45. Mundra P., Kumar M., Kumar K.K., Jayaraman V.K., and Kulkarni B.D. Using pseudo amino acid composition to predict protein subnuclear localization: approached with PSSM. Pattern Recogn. Lett. 28 (2007) 1610-1615
46. Scholkopf B., Sung K.K., Burges C.J.C., Girosi F., Niyogi P., Poggio T., and Vapnik V. Comparing support vector machines with Gaussian kernels to radial basis function classifiers. IEEE Trans. Sig. Proc. 45 (1997) 2758-2765
47. Shen H.B., and Chou K.C. Using optimized evidence-theoretic K-nearest neighbor classifier and pseudo-amino acid composition to predict membrane protein types. Biochem. Biophys. Res. Commun. 334 (2005) 288-292
48. Shen H.B., and Chou K.C. Predicting protein subnuclear location with optimized evidence-theoretic K-nearest classifier and pseudo amino acid composition. Biochem. Biophys. Res. Commun. 337 (2005) 752-756
49. Shen H.B., and Chou K.C. PseAAC: a flexible web server for generating various kinds of protein pseudo amino acid composition. Anal. Biochem. 373 (2007) 386-388
50. Shen H.B., Yang J., Liu X.J., and Chou K.C. Using supervised fuzzy clustering to predict protein structural classes. Biochem. Biophys. Res. Commun. 334 (2005) 577-581
51. Shen H.B., Yang J., and Chou K.C. Fuzzy KNN for predicting membrane protein types from pseudo-amino acid composition. J. Theor. Biol. 240 (2006) 9-13
52. Shi J.Y., Zhang S.W., Pan Q., Cheng Y.M., and Xie J. Prediction of protein subcellular localization by support vector machines using multi-scale energy and pseudo amino acid composition. Amino Acids 33 (2007) 69-74
53. Sun X.D., and Huang R.B. Prediction of protein structural classes using support vector machines. Amino Acids 30 (2006) 469-475
54. Wang S.Q., Yang J., and Chou K.C. Using stacked generalization to predict membrane protein types based on pseudo-amino acid composition. J. Theor. Biol. 242 (2006) 941-946
55. Xiao X., Shao S.H., Ding Y.S., Huang Z.D., Chen X.J., and Chou K.C. An application of gene comparative image for predicting the effect on replication ratio by HBV virus gene missense mutation. J. Theor. Biol. 235 (2005) 555-565
56. Xiao X., Shao S., Ding Y., Huang Z., and Chou K.C. Using cellular automata images and pseudo amino acid composition to predict protein subcellular location. Amino Acids 30 (2006) 49-54
57. Xiao X., Shao S.H., Huang Z.D., and Chou K.C. Using pseudo amino acid composition to predict protein structural classes: approached with complexity measure factor. J. Comput. Chem. 27 (2006) 478-482
58. Yan X.Q., Chao T.F., Tu K., Zhang Y., Xie L., Gong Y.H., Yuan J.G., Qiang B.Q., and Peng X.Z. Improving the prediction of human microRNA target genes by using ensemble algorithm. FEBS Lett. 581 (2007) 1587-1593
59. Zhang C.T., and Chou K.C. An optimization approach to predicting protein structural class from amino-acid-composition. Protein Sci. 1 (1992) 401-408
60. Zhang T.L., and Ding Y.S. Using pseudo amino acid composition and binary-tree support vector machines to predict protein structural classes. Amino Acids 33 (2007) 623-629
61. Zhang C.T., Chou K.C., and Maggiora G.M. Predicting protein structural classes from amino-acid-composition-application of fuzzy clustering. Protein Eng. 8 (1995) 425-435
62. Zhang S.W., Pan Q., Zhang H.C., Shao Z.C., and Shi J.Y. Prediction of protein homo-oligomer types by pseudo amino acid composition: approached with an improved feature extraction and Naive Bayes Feature Fusion. Amino Acids 30 (2006) 461-468
63. Zhang, T.L., Ding, Y.S., Shao, S.H., 2006b. Protein subcellular location prediction based on pseudo amino acid composition and immune genetic algorithm. Comput. Intell. Bioinform., Pt. 3, Proc. 4115, 534-542.
64. Zhang T.L., Ding Y.S., and Chou K.C. Prediction protein structural classes with pseudo-amino acid composition: approximate entropy and hydrophobicity pattern. J. Theor. Biol. 250 (2008) 186-193
65. Zhou G.P. An intriguing controversy over protein structural class prediction. J. Protein Chem. 17 (1998) 729-738
66. Zhou G.P., and Assa-Munt N. Some insights into protein structural class prediction. Proteins: Struct. Funct. Genet. 44 (2001) 57-59
67. Zhou G.P., and Cai Y.D. Predicting protease types by hybridizing gene ontology and pseudo amino acid composition. Proteins: Struct. Funct. Bioinform. 63 (2006) 681-684
68. Zhou G.F., Xu X.H., and Zhang C.T. A weighting method for predicting protein structural class from amino-acid-composition. Eur. J. Biochem. 210 (1992) 747-749
69. Zhou X.B., Chen C., Li Z.C., and Zou X.Y. Using Chou's amphiphilic pseudo-amino acid composition and support vector machine for prediction of enzyme subfamily classes. J. Theor. Biol. 248 (2007) 546-551
70. Zhou, X.B., Chen, C., Li, Z.C., Zou, X.Y., 2008. Improved prediction of subcellular location for apoptosis proteins by the dual-layer support vector machine. Amino Acids, in press, doi:10.1007/s00726-007-0608-y.