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Volumn 357, Issue 1, 2006, Pages 116-121

Predicting protein structural class with pseudo-amino acid composition and support vector machine fusion network

Author keywords

Amino acid composition; Fusion; Pair coupled amino acid composition; Protein structural class; Pseudo amino acid composition; Support vector machine

Indexed keywords

AMINO ACIDS; FUSION REACTIONS; SUPPORT VECTOR MACHINES;

EID: 33748287103     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2006.07.022     Document Type: Article
Times cited : (167)

References (50)
  • 1
    • 0017309766 scopus 로고
    • Structural patterns in globular proteins
    • Levitt M., and Chothia C. Structural patterns in globular proteins. Nature 261 (1976) 552-558
    • (1976) Nature , vol.261 , pp. 552-558
    • Levitt, M.1    Chothia, C.2
  • 2
    • 0026636320 scopus 로고
    • A correlation-coefficient method to predicting protein-structural classes from amino-acid compositions
    • 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
    • (1992) Eur. J. Biochem. , vol.207 , pp. 429-433
    • Chou, K.C.1    Zhang, C.T.2
  • 3
    • 0027076753 scopus 로고
    • A weighting method for predicting protein structural class from amino-acid composition
    • 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
    • (1992) Eur. J. Biochem. , vol.210 , pp. 747-749
    • Zhou, G.F.1    Xu, X.H.2    Zhang, C.T.3
  • 4
    • 0027080161 scopus 로고
    • An optimization approach to predicting protein structural class from amino-acid composition
    • 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
    • (1992) Protein Sci. , vol.1 , pp. 401-408
    • Zhang, C.T.1    Chou, K.C.2
  • 5
    • 0028121983 scopus 로고
    • Predicting protein-folding types by distance functions that make allowances for amino-acid interactions
    • 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
    • (1994) J. Biol. Chem. , vol.269 , pp. 22014-22020
    • Chou, K.C.1    Zhang, C.T.2
  • 6
    • 0028978517 scopus 로고
    • Predicting protein structural classes from amino-acid composition: application of fuzzy clustering
    • 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
    • (1995) Protein Eng. , vol.8 , pp. 425-435
    • Zhang, C.T.1    Chou, K.C.2    Maggiora, G.M.3
  • 7
    • 0029051959 scopus 로고
    • A novel approach to predicting protein structural classes in a (20-1)-D amino-acid composition space
    • 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
    • (1995) Proteins: Struct. Funct. Genet. , vol.21 , pp. 319-344
    • Chou, K.C.1
  • 8
    • 0030955263 scopus 로고    scopus 로고
    • Understanding the recognition of protein structural classes by amino acid composition
    • Bahar I., Atilgan A.R., Jernigan R.L., and Erman B. Understanding the recognition of protein structural classes by amino acid composition. Proteins 29 (1997) 172-185
    • (1997) Proteins , vol.29 , pp. 172-185
    • Bahar, I.1    Atilgan, A.R.2    Jernigan, R.L.3    Erman, B.4
  • 9
    • 54749084166 scopus 로고    scopus 로고
    • An intriguing controversy over protein structural class prediction
    • Zhou G.P. An intriguing controversy over protein structural class prediction. J. Protein Chem. 17 (1998) 729-738
    • (1998) J. Protein Chem. , vol.17 , pp. 729-738
    • Zhou, G.P.1
  • 10
    • 0033809190 scopus 로고    scopus 로고
    • Prediction of protein structural classes by neural network
    • Cai Y.D., and Zhou G.P. Prediction of protein structural classes by neural network. Biochimie 82 (2000) 783-785
    • (2000) Biochimie , vol.82 , pp. 783-785
    • Cai, Y.D.1    Zhou, G.P.2
  • 11
    • 2942601555 scopus 로고    scopus 로고
    • Support vector machines for predicting protein structural class
    • Cai Y.D., Liu X.J., Xu X.B., and Zhou G.P. Support vector machines for predicting protein structural class. BMC Bioinform. 2 (2001) 1-5
    • (2001) BMC Bioinform. , vol.2 , pp. 1-5
    • Cai, Y.D.1    Liu, X.J.2    Xu, X.B.3    Zhou, G.P.4
  • 12
    • 0035400226 scopus 로고    scopus 로고
    • Some insights into protein structural class prediction
    • Zhou G.P., and Assa-Munt N. Some insights into protein structural class prediction. Proteins: Struct. Funct. Genet. 44 (2001) 57-59
    • (2001) Proteins: Struct. Funct. Genet. , vol.44 , pp. 57-59
    • Zhou, G.P.1    Assa-Munt, N.2
  • 13
    • 22144498433 scopus 로고    scopus 로고
    • Using supervised fuzzy clustering to predict protein structural classes
    • 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
    • (2005) Biochem. Biophys. Res. Commun. , vol.334 , pp. 577-581
    • Shen, H.B.1    Yang, J.2    Liu, X.J.3    Chou, K.C.4
  • 15
    • 0034285487 scopus 로고    scopus 로고
    • Prediction of protein structural classes and subcellular locations
    • Chou K.C. Prediction of protein structural classes and subcellular locations. Curr. Protein Peptide Sci. 1 (2000) 171-208
    • (2000) Curr. Protein Peptide Sci. , vol.1 , pp. 171-208
    • Chou, K.C.1
  • 16
    • 26844545834 scopus 로고    scopus 로고
    • Progress in protein structural class prediction and its impact to bioinformatics and proteomics
    • Chou K.C. Progress in protein structural class prediction and its impact to bioinformatics and proteomics. Curr. Protein Peptide Sci. 6 (2005) 423-436
    • (2005) Curr. Protein Peptide Sci. , vol.6 , pp. 423-436
    • Chou, K.C.1
  • 17
    • 0032781417 scopus 로고    scopus 로고
    • Using pair-coupled amino acid composition to predict protein secondary structure content
    • Chou K.C. Using pair-coupled amino acid composition to predict protein secondary structure content. J. Protein Chem. 18 (1999) 473-480
    • (1999) J. Protein Chem. , vol.18 , pp. 473-480
    • Chou, K.C.1
  • 18
    • 0036051172 scopus 로고    scopus 로고
    • Prediction of protein structural class by amino acid and polypeptide composition
    • 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
    • (2002) Eur. J. Biochem. , vol.269 , pp. 4219-4225
    • Luo, R.Y.1    Feng, Z.P.2    Liu, J.K.3
  • 19
    • 33745093400 scopus 로고    scopus 로고
    • Prediction of protein structural classes using support vector machines
    • Sun X.D., and Huang R.B. Prediction of protein structural classes using support vector machines. Amino Acids 30 (2006) 469-475
    • (2006) Amino Acids , vol.30 , pp. 469-475
    • Sun, X.D.1    Huang, R.B.2
  • 20
    • 0035874091 scopus 로고    scopus 로고
    • Prediction of protein cellular attributes using pseudo-amino acid composition
    • Chou K.C. Prediction of protein cellular attributes using pseudo-amino acid composition. Proteins: Struct. Funct. Genet. 43 (2001) 246-255
    • (2001) Proteins: Struct. Funct. Genet. , vol.43 , pp. 246-255
    • Chou, K.C.1
  • 21
    • 33644889341 scopus 로고    scopus 로고
    • Using pseudo amino acid composition to predict protein structural classes: approached with complexity measure factor
    • 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
    • (2006) J. Comput. Chem. , vol.27 , pp. 478-482
    • Xiao, X.1    Shao, S.H.2    Huang, Z.D.3    Chou, K.C.4
  • 22
    • 0842330730 scopus 로고    scopus 로고
    • Correlations of amino acids in proteins
    • Du Q.S., Wei D.Q., and Chou K.C. Correlations of amino acids in proteins. Peptides 24 (2003) 1863-1869
    • (2003) Peptides , vol.24 , pp. 1863-1869
    • Du, Q.S.1    Wei, D.Q.2    Chou, K.C.3
  • 23
    • 33646568767 scopus 로고    scopus 로고
    • Amino acid principal component analysis (AAPCA) and its applications in protein structural class prediction
    • 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
    • (2006) J. Biomol. Struct. Dyn. , vol.23 , pp. 635-640
    • Du, Q.S.1    Jiang, Z.Q.2    He, W.Z.3    Li, D.P.4    Chou, K.C.5
  • 24
    • 3843117638 scopus 로고    scopus 로고
    • Predicting protein structural class by functional domain composition
    • Chou K.C., and Cai Y.D. Predicting protein structural class by functional domain composition. Biochem. Biophys. Res. Commun. 321 (2004) 1007-1009
    • (2004) Biochem. Biophys. Res. Commun. , vol.321 , pp. 1007-1009
    • Chou, K.C.1    Cai, Y.D.2
  • 25
    • 0038705861 scopus 로고    scopus 로고
    • Nearest neighbor algorithm for predicting protein subcellular location by combining functional domain composition and pseudo-amino acid composition
    • Cai Y.D., and Chou K.C. Nearest neighbor algorithm for predicting protein subcellular location by combining functional domain composition and pseudo-amino acid composition. Biochem. Biophys. Res. Commun. 305 (2003) 407-411
    • (2003) Biochem. Biophys. Res. Commun. , vol.305 , pp. 407-411
    • Cai, Y.D.1    Chou, K.C.2
  • 26
    • 14844285429 scopus 로고    scopus 로고
    • Using functional domain composition to predict enzyme family classes
    • Cai Y.D., and Chou K.C. Using functional domain composition to predict enzyme family classes. J. Proteome Res. 4 (2005) 109-111
    • (2005) J. Proteome Res. , vol.4 , pp. 109-111
    • Cai, Y.D.1    Chou, K.C.2
  • 27
    • 20844436424 scopus 로고    scopus 로고
    • Predicting enzyme subclass by functional domain composition and pseudo amino acid composition
    • 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
    • (2005) J. Proteome Res. , vol.4 , pp. 967-971
    • Cai, Y.D.1    Chou, K.C.2
  • 28
    • 22144470177 scopus 로고    scopus 로고
    • Boosting classifier for predicting protein domain structural class
    • Feng K.Y., Cai Y.D., and Chou K.C. Boosting classifier for predicting protein domain structural class. Biochem. Biophys. Res. Commun. 334 (2005) 213-217
    • (2005) Biochem. Biophys. Res. Commun. , vol.334 , pp. 213-217
    • Feng, K.Y.1    Cai, Y.D.2    Chou, K.C.3
  • 29
    • 28444439947 scopus 로고    scopus 로고
    • Using LogitBoost classifier to predict protein structural classes
    • 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
    • (2006) J. Theor. Biol. , vol.238 , pp. 172-176
    • Cai, Y.D.1    Feng, K.Y.2    Lu, W.C.3    Chou, K.C.4
  • 30
    • 24144433779 scopus 로고    scopus 로고
    • Fusion of classifiers for protein fold recognition
    • Nanni L. Fusion of classifiers for protein fold recognition. Neurocomputing 68 (2005) 315-321
    • (2005) Neurocomputing , vol.68 , pp. 315-321
    • Nanni, L.1
  • 31
    • 13244292990 scopus 로고    scopus 로고
    • A two-stage classifier for identification of protein-protein interface residues
    • Yan C., Dobbs D., and Honavar V. A two-stage classifier for identification of protein-protein interface residues. Bioinformatics 20 Suppl. 1 (2004) i371-i378
    • (2004) Bioinformatics , vol.20 , Issue.SUPPL. 1
    • Yan, C.1    Dobbs, D.2    Honavar, V.3
  • 32
    • 1542346418 scopus 로고    scopus 로고
    • A novel method for protein secondary structure prediction using dual-layer SVM and profiles
    • Guo J., Chen H., Sun Z.R., and Lin Y.L. A novel method for protein secondary structure prediction using dual-layer SVM and profiles. Proteins: Struct. Funct. Bioinform. 54 (2004) 738-743
    • (2004) Proteins: Struct. Funct. Bioinform. , vol.54 , pp. 738-743
    • Guo, J.1    Chen, H.2    Sun, Z.R.3    Lin, Y.L.4
  • 33
    • 14644440766 scopus 로고    scopus 로고
    • Prediction of protein relative solvent accessibility with a two-stage SVM approach
    • Nguyen M.N., and Rajapakse J.C. Prediction of protein relative solvent accessibility with a two-stage SVM approach. Proteins: Struct. Funct. Bioinform. 59 (2005) 30-37
    • (2005) Proteins: Struct. Funct. Bioinform. , vol.59 , pp. 30-37
    • Nguyen, M.N.1    Rajapakse, J.C.2
  • 34
    • 15944362593 scopus 로고    scopus 로고
    • Two-stage multi-class support vector machines to protein secondary structure prediction
    • Nguyen M.N., and Rajapakse J.C. Two-stage multi-class support vector machines to protein secondary structure prediction. Pacific Symp. Biocomp. (2005) 346-357
    • (2005) Pacific Symp. Biocomp. , pp. 346-357
    • Nguyen, M.N.1    Rajapakse, J.C.2
  • 35
    • 33646036734 scopus 로고    scopus 로고
    • Two-stage support vector regression approach for predicting accessible surface areas of amino acids
    • Nguyen M.N., and Rajapakse J.C. Two-stage support vector regression approach for predicting accessible surface areas of amino acids. Proteins: Struct. Funct. Bioinform. 63 (2006) 542-550
    • (2006) Proteins: Struct. Funct. Bioinform. , vol.63 , pp. 542-550
    • Nguyen, M.N.1    Rajapakse, J.C.2
  • 36
    • 0141815538 scopus 로고    scopus 로고
    • Predicting protein quaternary structure by pseudo amino acid composition
    • Chou K.C., and Cai Y.D. Predicting protein quaternary structure by pseudo amino acid composition. Proteins: Struct. Funct. Genet. 53 (2003) 282-289
    • (2003) Proteins: Struct. Funct. Genet. , vol.53 , pp. 282-289
    • Chou, K.C.1    Cai, Y.D.2
  • 37
    • 7444264582 scopus 로고    scopus 로고
    • Predicting subcellular localization of proteins by hybridizing functional domain composition and pseudo-amino acid composition
    • Chou K.C., and Cai Y.D. Predicting subcellular localization of proteins by hybridizing functional domain composition and pseudo-amino acid composition. J. Cell. Biochem. 91 (2004) 1197-1203
    • (2004) J. Cell. Biochem. , vol.91 , pp. 1197-1203
    • Chou, K.C.1    Cai, Y.D.2
  • 38
    • 22144487766 scopus 로고    scopus 로고
    • Using optimized evidence-theoretic K-nearest neighbor classifier and pseudo-amino acid composition to predict membrane protein types
    • 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
    • (2005) Biochem. Biophys. Res. Commun. , vol.334 , pp. 288-292
    • Shen, H.B.1    Chou, K.C.2
  • 39
    • 26844455291 scopus 로고    scopus 로고
    • Predicting protein subnuclear location with optimized evidence-theoretic K-nearest classifier and pseudo amino acid composition
    • 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
    • (2005) Biochem. Biophys. Res. Commun. , vol.337 , pp. 752-756
    • Shen, H.B.1    Chou, K.C.2
  • 40
    • 12744279642 scopus 로고    scopus 로고
    • Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes
    • Chou K.C. Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes. Bioinformatics 21 (2005) 10-19
    • (2005) Bioinformatics , vol.21 , pp. 10-19
    • Chou, K.C.1
  • 41
    • 33745076136 scopus 로고    scopus 로고
    • Prediction of protein homo-oligomer types by pseudo amino acid composition: approached with an improved feature extraction and naive Bayes feature fusion
    • 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
    • (2006) Amino Acids , vol.30 , pp. 461-468
    • Zhang, S.W.1    Pan, Q.2    Zhang, H.C.3    Shao, Z.C.4    Shi, J.Y.5
  • 42
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • Kyte J., and Doolittle R.F. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157 (1982) 105-132
    • (1982) J. Mol. Biol. , vol.157 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2
  • 43
    • 18344391868 scopus 로고    scopus 로고
    • Prediction of membrane protein types by incorporating amphipathic effects
    • Chou K.C., and Cai Y.D. Prediction of membrane protein types by incorporating amphipathic effects. J. Chem. Inform. Model. 45 (2005) 407-413
    • (2005) J. Chem. Inform. Model. , vol.45 , pp. 407-413
    • Chou, K.C.1    Cai, Y.D.2
  • 44
    • 34249753618 scopus 로고
    • Support-vector networks
    • Cortes C., and Vapnik V. Support-vector networks. Mach. Learn. 20 (1995) 273-297
    • (1995) Mach. Learn. , vol.20 , pp. 273-297
    • Cortes, C.1    Vapnik, V.2
  • 45
    • 23144436397 scopus 로고    scopus 로고
    • BhairPred: prediction of β-hairpins in a protein from multiple alignment information using ANN and SVM techniques
    • Kumar M., Bhasin M., Natt N.K., and Raghava G.P.S. BhairPred: prediction of β-hairpins in a protein from multiple alignment information using ANN and SVM techniques. Nucleic Acids Res. 33 (2005) W154-W159
    • (2005) Nucleic Acids Res. , vol.33
    • Kumar, M.1    Bhasin, M.2    Natt, N.K.3    Raghava, G.P.S.4
  • 46
    • 0037195776 scopus 로고    scopus 로고
    • Using functional domain composition and support vector machines for prediction of protein subcellular location
    • Chou K.C., and Cai Y.D. Using functional domain composition and support vector machines for prediction of protein subcellular location. J. Biol. Chem. 277 (2002) 45765-45769
    • (2002) J. Biol. Chem. , vol.277 , pp. 45765-45769
    • Chou, K.C.1    Cai, Y.D.2
  • 47
    • 0038636605 scopus 로고    scopus 로고
    • Support vector machines for predicting membrane protein types by using functional domain composition
    • Cai Y.D., Zhou G.P., and Chou K.C. Support vector machines for predicting membrane protein types by using functional domain composition. Biophys. J. 84 (2003) 3257-3263
    • (2003) Biophys. J. , vol.84 , pp. 3257-3263
    • Cai, Y.D.1    Zhou, G.P.2    Chou, K.C.3
  • 48
    • 33748335119 scopus 로고    scopus 로고
    • C.C. Chang, C.J. Lin, LIBSVM: A Library for Support Vector Machines [software], 2001, www.csie.ntu.edu.tw/~cjlin/libsvm.
  • 49
    • 0036532571 scopus 로고    scopus 로고
    • Switching between selection and fusion in combining classifiers: an experiment
    • Kuncheva L.I. Switching between selection and fusion in combining classifiers: an experiment. IEEE Trans. Syst. Man Cybern. B Cybern. 32 (2002) 146-156
    • (2002) IEEE Trans. Syst. Man Cybern. B Cybern. , vol.32 , pp. 146-156
    • Kuncheva, L.I.1
  • 50
    • 32644441676 scopus 로고    scopus 로고
    • Prediction of protein structural class with Rough Sets
    • 10.1186/1471-2105-720
    • 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) 10.1186/1471-2105-720
    • (2006) BMC Bioinform. , vol.7
    • Cao, Y.F.1    Liu, S.2    Zhang, L.D.3    Qin, J.4    Wang, J.5    Tang, K.X.6


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