A novel feature representation method based on Chou's pseudo amino acid composition for protein structural class prediction

Computational Biology and Chemistry

Volumn 34, Issue 5-6, 2010, Pages 320-327

  Sahu, Sitanshu Sekhar ^a   Panda, Ganapati ^b  

^a NATIONAL INSTITUTE OF TECHNOLOGY   (India)

^b INDIAN INSTITUTE OF TECHNOLOGY BHUBANESWAR   (India)

Author keywords

AAC; AmPseAAC; DCT; Protein domain; RBFNN; Structural class

Indexed keywords

AAC; AMPSEAAC; DCT; PROTEIN DOMAIN; RBFNN; STRUCTURAL CLASS;

AMINO ACIDS; CLASSIFICATION (OF INFORMATION); FORECASTING; RADIAL BASIS FUNCTION NETWORKS;

PROTEINS;

AMINO ACID; PROTEIN;

ALGORITHM; ARTICLE; CHEMISTRY; CLASSIFICATION; GENETICS; METHODOLOGY; PROTEIN DATABASE; SEQUENCE ANALYSIS;

ALGORITHMS; AMINO ACIDS; DATABASES, PROTEIN; PROTEINS; SEQUENCE ANALYSIS, PROTEIN;

EID: 78649324596     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2010.09.002     Document Type: Article

References (63)

1. M.S. Ahmad Iris recognition using the discrete cosine transform and artificial neural networks J. Comput. Sci. 5 4 2009 369 373
2. N. Ahmed, T. Natarajan, and K.R. Rao Discrete cosine transforms IEEE Trans. Comput. C-32 1974 90 93
3. Y. Cai, and G. Zhou Prediction of protein structural classes by neural network Biochimie 82 8 2000 783 785
4. Y.D. Cai, Y.X. Li, and K.C. Chou Using neural networks for prediction of domain structural classes Biochim. Biophys. Acta 1476 2000 1 2
5. Y.D. Cai, X.J. Liu, X. Xu, and G.P. Zhou Support vector machines for predicting protein structural class BMC Bioinformatics 2 2001 3
6. Y.F. Cao, S. Liu, L. Zhang, J. Qin, J. Wang, and K.X. Tang Prediction of protein structural class with rough sets BMC Bioinformatics 7 2006 1 6
7. J.M. Chandonia, and M. Karplus Neural networks for secondary structure and structural class prediction Protein Sci. 4 1995 275 285
8. C. Chao, Z. Xibin, T. Yuanxin, Z. Xiaoyong, and C. Peixiang Predicting protein structural class with pseudo-amino acid composition and support vector machine fusion network Anal. Biochem. 357 2006 116 121
9. K.E. Chen, A.K. Lukasz, and J. Ruan Prediction of protein structural class using Novel Evolutionary Collocation-based sequence representation J. Comput. Chem. 29 10 2007 1596 1604
10. C. Chen, L. Chen, X. Zou, and P. Cai Prediction of protein secondary structure content by using the concept of Chou's pseudo amino acid composition and support vector machine Protein Peptide Lett. 16 2009 27 31
11. K.C. Chou Review: Low-frequency collective motion in biomacromolecules and its biological functions Biophys. Chem. 30 1988 3 48
12. K.C. Chou Low-frequency resonance and cooperativity of hemoglobin Trends Biochem. Sci. 14 1989 212
13. K.C. Chou A novel approach to predicting protein structural classes in a (20-1)-D amino acid composition space Proteins 21 4 1995 319 344
14. K.C. Chou A key driving force in determination of protein structural classes Biochem. Biophys. Res. Commun. 264 1999 216 224
15. K.C. Chou Prediction of protein structural classes and subcellular locations Curr. Protein Pept. Sci. 1 2 2000 171 208
16. K.C. Chou Prediction of protein cellular attributes using pseudo amino acid composition Proteins 43 2001 246 255
17. K.C. Chou Using amphiphilic pseudo amino acid composition to predict enzyme Bioinformatics 21 2005 10 19
18. K.C. Chou Pseudo amino acid composition and its applications in bioinformatics, proteomics and system biology Curr. Proteomics 6 2009 262 274
19. K.C. Chou, and G.M. Maggiora Domain structural class prediction Prot. Eng. 11 7 1998 523 538
20. K.C. Chou, and H.B. Shen Review: Recent progresses in protein subcellular location prediction Anal. Biochem. 370 2007 1 16
21. K.C. Chou, and H.B. Shen Review: Recent advances in developing web-servers for predicting protein attributes Nat. Sci. 2 2009 63 92 (Openly accessible at http://www.scirp.org/journal/NS/ )
22. K.C. Chou, and H.B. Shen Plant-mPLoc: a top-down strategy to augment the power for predicting plant protein subcellular localization PLoS ONE 5 2010 e11335
23. K.C. Chou, and H.B. Shen A new method for predicting the subcellular localization of eukaryotic proteins with both single and multiple sites: Euk-mPLoc 2.0 PLoS ONE 5 2010 e9931
24. K.C. Chou, and C.T. Zhang Predicting protein folding types by distance functions that make allowances for amino acid interactions J. Biol. Chem. 269 35 1994 22014 22020
25. K.C. Chou, and C.T. Zhang Review: Prediction of protein structural classes Crit. Rev. Biochem. Mol. Biol. 30 1995 275 349
26. Y.S. Ding, T.L. Zhang, and K.C. Chou Prediction of protein structure classes with pseudo amino acid composition and fuzzy support vector machines network Protein Peptide Lett. 14 2007 811 815
27. H. Ding, L. Luo, and H. Lin Prediction of cell wall lytic enzymes using Chou's amphiphilic pseudo amino acid composition Protein Peptide Lett. 16 2009 351 355
28. Q.S. Du, Z.Q. Jiang, W.Z. He, D.P. Li, and K.C. Chou Amino acid principal component analysis (AAPCA) and its applications in protein structural class prediction J. Bimol. Struct. Dynam. 23 2006 635 640
29. M. Esmaeili, H. Mohabatkar, and S. Mohsenzadeh Using the concept of Chou's pseudo amino acid composition for risk type prediction of human papillomaviruses J. Theor. Biol. 263 2010 203 209
30. K.Y. Feng, Y.D. Cai, and K.C. Chou Boosting classifier for predicting protein domain structural class Biochem. Biophys. Res. Commun. 334 1 2005 213 217
31. G. Gordon Extrinsic electromagnetic fields, low frequency (phonon) vibrations, and control of cell function: a non-linear resonance system J. Biomed. Sci. Eng. 1 2008 152 156 (Open accessible at http://www.srpublishing. org/journal/jbise/ )
32. T.P. Hopp, and K.R. Woods Prediction of protein antigenic determinants from amino acid sequences J. Proc. Natl. Acad. Sci. U.S.A. 78 1981 3824 3828
33. X. Jiang, R. Wei, T.L. Zhang, and Q. Gu Using the concept of Chou's pseudo amino acid composition to predict apoptosis proteins subcellular location: an approach by approximate entropy Protein Peptide Lett. 15 2008 392 396
34. S. Kannan, A.M. Hauth, and G. Burger Function prediction of hypothetical proteins without sequence similarity to proteins of known function Protein Peptide Lett. 15 2008 1107 1116
35. P. Klein, and C. Delisi Prediction of protein structural class from the amino acid sequence Biopolymers 25 9 1986 1659 1672
36. M. Levitt, and C. Chothia Structural patterns in globular proteins Nature 261 5561 1976 552 558
37. Z.C. Li, X.B. Zhou, Y.R. Lin, and X.Y. Zou Prediction of protein structural class by coupling improved genetic algorithm and support vector machine Amino Acids 35 2008 581 590
38. H. Lin The modified Mahalanobis discriminant for predicting outer membrane proteins by using Chou's pseudo amino acid composition J. Theor. Biol. 252 2008 350 356
39. H. Liu, W. Meng, and K.C. Chou Low-frequency Fourier spectrum for predicting membrane protein types Biochem. Biophys. Res. Commun. 336 2005 737 739
40. H. Liu, J. Yang, W. Meng, X. Li, and K.C. Chou Using Fourier spectrum analysis and pseudo amino acid composition for prediction of membrane protein types Protein J. 24 6 2005
41. T. Liu, X. Zheng, and W. Jun Prediction of protein structural class using a complexity-based distance measure Amino acids 2009
42. R.Y. Luo, Z.P. Feng, and J.K. Liu Prediction of protein structural class by amino acid and polypeptide composition Eur. J. Biochem. 269 2002 4219 4225
43. A. Madkan, M. Blank, E. Elson, K.C. Chou, M.S. Geddis, and R. Goodman Steps to the clinic with ELF EMF Nat. Sci. 1 2009 157 165 (Openly accessible at http://www.scirp.org/journal/NS/ )
44. W. Meng, J. Yang, G.-P. Liu, Z.J. Xu, and K.C. Chou Weighted-support vector machines for predicting membrane protein types based on pseudo-amino acid composition Protein Eng. Design Select. 17 6 2004 509 516
45. H. Nakashima, K. Nishikawa, and T. Ooi The folding type of a protein is relevant to its amino acid composition J. Biochem. 1986 153 159
46. J. Neves, M. Santos, and J. Machado Feature extraction from tumor gene expression profiles using DCT and DFT EPIA 2007 485 496
47. J. Park, and J.W. Sandberg Universal approximation using radial basis function network Neural Comput. 3 1991 246 257
48. R. Rao, and S. Lakshminarayanan Variable predictive model based classification algorithm for effective separation of protein structural classes Comput. Biol. Chem. 32 2008 302 306
49. J. Samad, A. Parviz, J. Mina, and B.A. Ebrahim Novel two-stage hybrid neural discriminant model for predicting proteins structural class Biophys. Chem. 2007 87 93
50. S.R. Samantray, P.K. Dash, and G. Panda Fault classification and location using HS-transform and radial basis function neural network Electric Power Syst. Res. 76 9-10 2006 897 905
51. H.B. Shen, J. Yang, X.J. Liu, and K.C. Chou Using supervised fuzzy clustering to predict protein structural classes Biochem. Biophys. Res. Commun. 334 2 2005 577
52. M. Shigeki, H. Satoru, A. Toshio, and K. Ryoichi Spectral analysis of amino acid sequence. I. Intrinsic membrane proteins J. Phys. Soc. Jpn. 53 1984 4083 4090
53. X.D. Sun, and R.B. Huang Prediction of protein structural classes using support vector machine Amino Acids 30 2006 469 475
54. C. Tanford Contribution of hydrophobic interactions to the stability of the globular conformation of proteins J. Am. Chem. Soc. 84 1962 4240 4274
55. X. Xiao, S. Shi-Huang, Z. Huang, and K.C. Chou Using pseudo amino acid composition to predict protein structural classes: approached with complexity measure factor J. Comput. Chem. 27 2006 478 482
56. C. Yu-Dong, K.Y. Feng, W.C. Lu, and K.C. Chou Using LogitBoost classifier to predict protein structural classes J. Theor. Biol. 238 2006 172 176
57. Y.H. Zeng, Y.Z. Guo, R.Q. Xiao, L. Yang, L.Z. Yu, and M.L. Li Using the augmented Chou's pseudo amino acid composition for predicting protein submitochondria locations based on auto covariance approach J. Theor. Biol. 259 2009 366 372
58. T.L. Zhan, and Y.S. Ding Using pseudo amino acid composition and binary-tree support vector machines to predict protein structural classes Amino Acids 33 2007 623 629
59. Li. Zhan-Chao, X.B. Zhou, and Z. Dai Prediction of protein structural classes by Chou's pseudo amino acid composition: approached using continuous wavelet transform and principal component analysis Amino Acids 2008
60. T.L. Zhang, Y.S. Ding, and K.C. Chou Prediction protein structural classes with pseudo-amino acid composition: approximate entropy and hydrophobicity pattern J. Theor Biol. 250 2008 186 193
61. G.P. Zhou An intriguing controversy over protein structural class prediction J. Protein Chem. 17 8 1998 729 738
62. G.P. Zhou, and N. Assa-Munt Some insights into protein structural class prediction Proteins 44 1 2001 57 59
63. X.B. Zhou, C. Chen, Z.C. Li, and X.Y. Zou Using Chou's amphiphilic pseudo amino acid composition and support vector machine for prediction of enzyme subfamily classes J. Theor Biol. 248 2004 546 551