High-accuracy prediction of protein structural classes using PseAA structural properties and secondary structural patterns

Biochimie

Volumn 101, Issue 1, 2014, Pages 104-112

  Wang, Junru ^a   Li, Yan ^a   Liu, Xiaoqing ^b   Dai, Qi ^a   Yao, Yuhua ^a   He, Pingan ^a  

^a ZHEJIANG SCI TECH UNIVERSITY   (China)

^b HANGZHOU DIANZI UNIVERSITY   (China)

Author keywords

Local structural correlation; Long range structural property; Protein structural class prediction; PseAAs; Support vector machine

Indexed keywords

PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; CHEMICAL PHENOMENA; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; PROTEIN DATABASE; PROTEIN SECONDARY STRUCTURE; SEQUENCE ANALYSIS; SUPPORT VECTOR MACHINE;

ALGORITHMS; AMINO ACID SEQUENCE; COMPUTER SIMULATION; DATABASES, PROTEIN; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MODELS, MOLECULAR; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SEQUENCE ANALYSIS, PROTEIN; SUPPORT VECTOR MACHINES;

EID: 84899462085     PISSN: 03009084     EISSN: 61831638     Source Type: Journal    
DOI: 10.1016/j.biochi.2013.12.021     Document Type: Article

References (54)

1. P. Klein, and C. Delisi Prediction of protein structural class from the amino-acid sequence Biopolymers 25 1986 1659 1672
2. K.C. Chou Structural bioinformatics and its impact to biomedical science and drug discovery Front. Med. Chem. 3 2006 455 502
3. M. Levitt, and C. Chothia Structural patterns in globular proteins Nature 261 1976 552 558
4. 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. 32 2004 D226 D229
5. A.G. Murzin, S.E. Brenner, T. Hubbard, and C. Chothia SCOP: a structural classification of protein database for the investigation of sequence and structures J. Mol. Biol. 247 1995 536 540
6. P. Ferragina, R. Giancarlo, V. Greco, G. Manzini, and G. Valiente Compression-based classification of biological sequences and structures via the universal similarity metric: experimental assessment BMC Bioinf. 8 2007 252
7. Q. Dai, and T.M. Wang Comparison study on k-word statistical measures for protein: from sequence to 'sequence space' BMC Bioinf. 9 2008 394
8. C. Chen, Y. Tian, X. Zou, P. Cai, and J. Mo Using pseudo-amino acid composition and support vector machine to predict protein structural class J. Theor. Biol. 243 2006 444 448
9. K. Chou Review: prediction of protein structural classes and subcellular locations Curr. Protein. Pept. Sci. 1 2000 171 208
10. K.D. Kedarisetti, L.A. Kurgan, and S. Dick Classifier ensembles for protein structural class prediction with varying homology Biochem. Biophys. Res. Commun. 348 2006 981 988
11. M.J. Mizianty, and L. Kurgan Modular prediction of protein structural classes from sequences of twilight-zone identity with predicting sequences BMC Bioinf. 10 2009 414 438
12. P. Klein, and C. Delisi Prediction of protein structural class from amino acid sequence Biopolymers 25 1986 1659 1672
13. K. Chou A key driving force in determination of protein structural classes Biochem. Biophys. Res. Commun. 264 1999 216 224
14. T.L. Zhang, Y.S. Ding, and K. Chou Prediction protein structural classes with pseudo-amino acid composition: approximate entropy and hydrophobicity pattern J. Theor. Biol. 250 2008 186 193
15. 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
16. X.D. Sun, and R.B. Huang Prediction of protein structural classes using support vector machines Amino Acids 30 2006 469 475
17. Y.S. Ding, T.L. Zhang, and K.C. Chou Prediction of protein structure classes with pseudo amino acid composition and fuzzy support vector machine network Protein. Pept. Lett. 14 2007 811 815
18. K. Chou, and Y. Cai Prediction of protein subcellular locations by GO-FunD-PseAA predictor Biochem. Biophys. Res. Commun. 321 2004 1007 1009
19. K. Chen, L.A. Kurgan, and J. Ruan Prediction of protein structural class using novel evolutionary collocation based sequence representation J. Comput. Chem. 29 2008 1596 1604
20. K.C. Chou Prediction of protein cellular attributes using pseudo amino acid composition Proteins Struct. Funct. Genet. 43 2001 246 255
21. H.B. Shen, and K.C. Chou PseAAC: a flexible web-server for generating various kinds of protein pseudo amino acid composition Anal. Biochem. 373 2008 386 388
22. H. Liu, M. Wang, and K.C. Chou Low-frequency Fourier spectrum for predicting membrane protein types Biochem. Biophys. Res. Commun. 336 2005 737 739
23. X. Xiao, S.H. Shao, Z.D. Huang, and K. Chou Using pseudo amino acid composition to predict protein structural classes: approached with complexity measure factor J. Comput. Chem. 27 2006 478 482
24. H. Lin, and Q.Z. Li Using pseudo amino acid composition to predict protein structural class: approached by incorporating 400 dipeptide components J. Comput. Chem. 28 2007 1463 1466
25. X. Xiao, W.Z. Lin, and K.C. Chou Using grey dynamic modeling and pseudo amino acid composition to predict protein structural classes J. Comput. Chem. 29 2008 2018 2024
26. L.A. Kurgan, and L. Homaeian Prediction of structural classes for protein sequences and domains-Impact of prediction algorithms, sequence representation and homology, and test procedures on accuracy Pattern Recogn. 39 2006 2323 2343
27. L. Kurgan, K. Cios, and K. Chen SCPRED: accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences BMC Bioinf. 9 2008 226 240
28. C. Zheng, and L. Kurgan Prediction of beta-turns at over 80% accuracy based on an ensemble of predicted secondary structures and multiple alignments BMC Bioinf. 9 2008 430
29. T. Liu, and C.Z. Jia A high-accuracy protein structural class prediction algorithm using predicted secondary structural information J. Theor. Biol. 267 3 2010 272 275
30. S.L. Zhang, S.Y. Ding, and T.M. Wang High-accuracy prediction of protein structural class for low-similarity sequences based on predicted secondary structure Biochimie 93 2011 710 714
31. U. Hobohm, and C. Sander Enlarged representative set of protein structures Protein Sci. 3 1994 522 524
32. L. Kurgan, and K. Chen Prediction of protein structural class for the twilight zone sequences Biochem. Biophys. Res. Commun. 357 2007 453 460
33. N. Liu, and T. Wang Protein-based phylogenetic analysis by using hydropathy profile of amino acids FEBS. Lett. 580 2006 5321 5327
34. K.C. Chou, and Y.D. Cai Predicting protein quaternary structure by pseudo amino acid composition Proteins Struct. Funct. Genet. 53 2003 282 289
35. K.C. Chou, and Y.D. Cai Predicting subcellular localization of proteins by hybridizing functional domain composition and pseudo-amino acid composition J. Cell. Biochem. 91 2004 1197 1203
36. H.B. Shen, and K.C. Chou 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
37. H.B. Shen, and K.C. Chou Predicting protein subnuclear location with optimized evidence - theoretic K-nearest classifier and pseudo amino acid composition Biochem. Biophys. Res. Commun. 337 2005 752 756
38. K.C. Chou Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes Bioinformatics 21 2005 10 19
39. S.W. Zhang, Q. Pan, H.C. Zhang, Z.C. Shao, and J.Y. Shi 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
40. D.B. Wetlaufer Nucleation, rapid folding, and globular intrachain regions in proteins Proc. Natl. Acad. Sci. USA 70 1973 697 701
41. J.S. Richardson The anatomy and taxonomy of protein structure Adv. Protein. Chem. 34 1981 167 339
42. D.T. Jones Protein secondary structure prediction based on position specific scoring matrices J. Mol. Biol. 292 1999 195 202
43. L.F. Luo, and X.Q. Li Recognition and architecture of the framework structure of protein Proteins 39 2000 9 25
44. V. Vapnik The Nature of Statistical Learning Theory 2000 Springer Verlag
45. Y. Cai, X. Liu, X. Xu, and K. Chou Prediction of protein structural classes by support vector machines Comput. Chem. 26 2002 293 296
46. K. Chou, and H. Shen Recent progress in protein subcellular location prediction Anal. Biochem. 370 2007 1 16
47. Z. Yuan, T.L. Bailey, and R.D. Teasdale Prediction of protein B-factor profiles Proteins 58 2005 905 912
48. M.J. Mizianty, and L. Kurgan Meta prediction of protein crystallization propensity Biochem. Biophys. Res. Commun. 390 2009 10 15
49. J.Y. Yang, Z.L. Peng, and X. Chen Prediction of protein structural classes for low-homology sequences based on predicted secondary structure BMC Bioinf. 11 2010 S9
50. Q. Dai, L. Wu, and L.H. Li Improving protein structural class prediction using novel combined sequence information and predicted secondary structural features J. Comput. Chem. 32 2011 3393 3398
51. T.G. Liu, X.Q. Zheng, and J. Wang Prediction of protein structural class for low-similarity sequences Biochimie 92 2010 1330 1334
52. S.Y. Ding, S.L. Zhang, Y. Li, and T.M. Wang A novel protein structural classes prediction method based on predicted secondary structure Biochimie 94 2012 1166 1171
53. X.Y. Xia, M. Ge, Z.X. Wang, and X.M. Pan Accurate prediction of protein structural class PLoS One 7 2012 e37653
54. T.G. Liu, X.B. Geng, X.Q. Zheng, R.S. Li, and J. Wang Accurate prediction of protein structural class using auto covariance transformation of PSI-BLAST profiles Amino Acids 42 2012 2243 2249