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Articles

Using principal component analysis and support vector machine to predict protein structural class for low-similarity sequences via PSSM

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Pages 1138-1146 | Received 26 Sep 2011, Published online: 18 Apr 2012

References

  • Altschul , S.F. , Madden , T.L. , Schaffer , A.A. , Zhang , J. , Zhang , Z. , Miller , W. and Lipman , D.J. 1997 . Gapped BLAST and PSI-BLAST: A new generation of protein database search programs . Nucleic Acids Research , 25 : 3389 – 3402 .
  • Anand , A. , Pugalenthi , G. and Suganthan , P.N. 2008 . Predicting protein structural class by SVM with class-wise optimized features and decision probabilities . Journal of Theoretical Biology , 253 : 375 – 380 .
  • Bastien , O. 2008 . A simple derivation of the distribution of pairwise local protein sequence alignment scores . Evolutionary Bioinformatics , 4 : 41 – 45 .
  • Bastien , O. , Ortet , P. , Roy , S. and Marechal , E. 2005 . A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities . BMC Bioinformatics , 6 : 49
  • Bastien , O. , Roy , S. and Marechal , E. 2005 . Construction of non-symmetric substitution matrices derived from proteomes with biased amino acid distributions . Comptes Rendus Biologies , 328 : 445 – 453 .
  • Cai , Y.D. , Feng , K.Y. , Lu , W.C. and Chou , K.C. 2006 . Using LogitBoost classifier to predict protein structural classes . Journal of Theoretical Biology , 238 : 172 – 176 .
  • Cai , Y.D. , Liu , X.J. , Xu , X.B. and Chou , K.C. 2002 . Prediction of protein structural classes by support vector machines . Journal of Computational Chemistry , 26 : 293 – 296 .
  • Cai , Y.D. , Liu , X.J. , Xu , X. and Zhou , G.P. 2001 . Support vector machines for predicting protein structural class . BMC Bioinformatics , 2 : 3
  • Cai , Y.D. and Zhou , G.P. 2000 . Prediction of protein structural classes by neural network . Biochimie , 82 : 783 – 785 .
  • Cao , Y.F. , Liu , S. , Zhang , L.D. , Qin , J. , Wang , J. and Tang , K.X. 2006 . Prediction of protein structural class with rough sets . BMC Bioinformatics , 7 : 20
  • Chang, C.C., & Lin, C.J. (2001). LIBSVM: A library for support vector machines. http://www.csie.ntu.edu.tw/∼cjlin/libsvm
  • Chang , J.M. , Su , E.C. , Lo , A. , Chiu , H.S. , Sung , T.Y. and Hsu , W.L. 2008 . PSLDoc: Protein subcellular localization prediction based on gapped-dipeptides and probabilistic latent semantic analysis . Proteins , 72 : 693 – 710 .
  • Chen , K. , Kurgan , L.A. and Ruan , J.S. 2008 . Prediction of protein structural class using novel evolutionary collocation-based sequence representation . Journal of Computational Chemistry , 29 : 1596 – 1604 .
  • Chen , C. , Tian , Y.X. , Zou , X.Y. , Cai , P.X. and Mo , J.Y. 2006 . Using pseudo-amino acid composition and support vector machine to predict protein structural class . Journal of Theoretical Biology , 243 : 444 – 448 .
  • Chou , K.C. 2004 . Structural bioinformatics and its impact to biomedical science . Current Medicinal Chemistry , 11 : 2105 – 2134 .
  • Chou , K.C. 2005 . Progress in protein structural class prediction and its impact to bioinformatics and proteomics . Current Protein and Peptide Science , 6 : 423 – 436 .
  • Chou , K.C. 2011 . Some remarks on protein attribute prediction and pseudo amino acid composition . Journal of Theoretical Biology , 273 : 236 – 247 .
  • Chou , K.C. 1999 . A key driving force in determination of protein structural classes . Biochemical and Biophysical Research Communications , 264 : 216 – 224 .
  • Chou , K.C. 2001 . Prediction of protein cellular attributes using pseudo-amino acid composition . Proteins , 43 : 246 – 255 .
  • Chou , K.C. and Cai , Y.D. 2004 . Predicting protein structural class by functional domain composition . Biochemical and Biophysical Research Communications , 321 : 1007 – 1009 .
  • Chou , K.C. and Shen , H.B. 2007 . MemType-2L: a web server for predicting membrane proteins and their types by incorporating evolution information through Pse-PSSM . Biochemical and Biophysical Research Communications , 360 : 339 – 345 .
  • Chou , K.C. and Shen , H.B. 2007 . Recent progress in protein subcellular location prediction . Analytical Biochemistry , 370 : 1 – 16 .
  • Chou , K.C. and Zhang , C.T. 1995 . Prediction of protein structural classes . Critical Reviews in Biochemistry and Molecular Biology , 30 : 275 – 349 .
  • Costantini , S. and Facchiano , A.M. 2009 . Prediction of the protein structural class by specific peptide frequencies . Biochimie , 91 : 226 – 229 .
  • Deschavanne , P. and Tuffery , P. 2008 . Exploring an alignment free approach for protein classification and structural class prediction . Biochimie , 90 : 615 – 625 .
  • Ding , Y.S. , Zhang , T.L. and Chou , K.C. 2007 . Prediction of protein structure classes with pseudo amino acid composition and fuzzy support vector machine network . Protein and Peptide Letters , 14 : 811 – 815 .
  • Dong , Q.W. , Zhou , S.G. and Guan , J.H. 2009 . A new taxonomy-based protein fold recognition approach based on autocross-covariance transformation . Bioinformatics , 25 : 2655 – 2662 .
  • Dou , Y. , Geng , X. , Gao , H. , Yang , J. , Zheng , X. and Wang , J. 2011 . Sequence conservation in the prediction of catalytic sites . Protein Journal , 30 : 229 – 239 .
  • Feng , K.Y. , Cai , Y.D. and Chou , K.C. 2005 . Boosting classifier for predicting protein domain structural class . Biochemical and Biophysical Research Communications , 334 : 213 – 217 .
  • Hua , S. and Sun , Z. 2001 . Support vector machine approach for protein subcellular localization prediction . Bioinformatics , 17 : 721 – 728 .
  • Jin , L.X. , Fang , W.W. and Tang , H.W. 2003 . Prediction of protein structural classes by a new measure of information discrepancy . Computational Biology and Chemistry , 27 : 373 – 380 .
  • Jolliffe , I.T. 1986 . Principal component analysis , New York , NY : Springer .
  • Kaur , H. and Raghava , G.P. 2003a . A neural-network based method for prediction of gamma-turns in proteins from multiple sequence alignment . Protein Science , 12 : 923 – 929 .
  • Kaur , H. and Raghava , G.P. 2003b . Prediction of beta-turns in proteins from multiple alignment using neural network . Protein Science , 12 : 627 – 634 .
  • Kedarisetti , K.D. , Kurgan , L. and Dick , S. 2006 . A comment on “Prediction of protein structural classes by a new measure of information discrepancy” . Computational Biology and Chemistry , 30 : 393 – 394 .
  • Kedarisetti , K.D. , Kurgan , L. and Dick , S. 2006 . Classifier ensembles for protein structural class prediction with varying homology . Biochemical and Biophysical Research Communications , 348 : 981 – 988 .
  • Kurgan , L. and Chen , K. 2007 . Prediction of protein structural class for the twilight zone sequences . Biochemical and Biophysical Research Communications , 357 : 453 – 460 .
  • Kurgan , L. , Cios , K. and Chen , K. 2008 . SCPRED: Accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences . BMC Bioinformatics , 9 : 226
  • Kurgan , L.A. and Homaeian , L. 2006 . Prediction of structural classes for protein sequences and domains--impact of prediction algorithms, sequence representation and homology, and test procedures on accuracy . Pattern Recognition , 39 : 2323 – 2343 .
  • Kurgan , L.A. , Zhang , T. , Zhang , H. , Shen , S.Y. and Ruan , J.S. 2008 . Secondary structure-based assignment of the protein structural classes . Amino Acids , 35 : 551 – 564 .
  • Li , Z.C. , Zhou , X.B. , Dai , Z. and Zou , X.Y. 2009 . Prediction of protein structural classes by Chou’s pseudo amino acid composition: Approached using continuous wavelet transform and principal component analysis . Amino Acids , 37 : 415 – 425 .
  • Lin , H. and Li , Q.Z. 2007 . Using pseudo amino acid composition to predict protein structural class: Approached by incorporating 400 dipeptide components . Journal of Computational Chemistry , 28 : 1463 – 1466 .
  • Liu, T., Geng, X., Zheng, X., Li, R., & Wang, J. (2011). Accurate prediction of protein structural class using auto covariance transformation of PSI-BLAST profiles. Amino acids. doi: 10.1007/s00726-011-0964-5.
  • Liu , T. and Jia , C. 2010 . A high-accuracy protein structural class prediction algorithm using predicted secondary structural information . Journal of Theoretical Biology , 267 : 272 – 275 .
  • Liu , T. , Zheng , X. and Wang , J. 2010 . Prediction of protein structural class for low-similarity sequences using support vector machine and PSI-BLAST profile . Biochimie , 92 : 1330 – 1334 .
  • Luo , R.Y. , Feng , Z.P. and Liu , J.K. 2002 . Prediction of protein structural class by amino acid and polypeptide composition . European Journal of Biochemistry , 269 : 4219 – 4225 .
  • Mizianty , M.J. and Kurgan , L. 2009 . Modular prediction of protein structural classes from sequences of twilight-zone identity with predicting sequences . BMC Bioinformatics , 10 : 414
  • Nakashima , H. , Nishikawa , K. and Ooi , T. 1986 . The folding type of a protein is relevant to the amino acid composition . Journal of Biochemistry , 99 : 153 – 162 .
  • Pu , X. , Guo , J. , Leung , H. and Lin , Y. 2007 . Prediction of membrane protein types from sequences and position-specific scoring matrices . Journal of Theoretical Biology , 247 : 259 – 265 .
  • Qiu , J.D. , Luo , S.H. , Huang , J.H. and Liang , R.P. 2009 . Using support vector machines for prediction of protein structural classes based on discrete wavelet transform . Journal of Computational Chemistry , 30 : 1344 – 1350 .
  • Rashid , M. , Saha , S. and Raghava , G.P. 2007 . Support Vector Machine-based method for predicting subcellular localization of mycobacterial proteins using evolutionary information and motifs . BMC Bioinformatics , 8 : 337
  • Shen , H.B. and Chou , K.C. 2007 . Nuc-PLoc: A new web-server for predicting protein subnuclear localization by fusing PseAA composition and PsePSSM . Protein Engineering, Design & Selection , 20 : 561 – 567 .
  • Shen , H.B. and Chou , K.C. 2009 . Predicting protein fold pattern with functional domain and sequential evolution information . Journal of Theoretical Biology , 256 : 441 – 446 .
  • Shen , H.B. and Chou , K.C. 2005 . Predicting protein subnuclear location with optimized evidence-theoretic K-nearest classifier and pseudo amino acid composition . Biochemical and Biophysical Research Communications , 337 : 752 – 756 .
  • Shen , H.B. , Yang , J. , Liu , X.J. and Chou , K.C. 2005 . Using supervised fuzzy clustering to predict protein structural classes . Biochemical and Biophysical Research Communications , 334 : 577 – 581 .
  • Sommer , I. , Rahnenfuhrer , J. , Domingues , F.S. , de Lichtenberg , U. and Lengauer , T. 2004 . Prediction protein structure classes from function predictions . Bioinformatics , 20 : 770 – 776 .
  • Sun , X.D. and Huang , R.B. 2006 . Prediction of protein structural classes using support vector machines . Amino Acids , 30 : 469 – 475 .
  • Wang , Z.X. and Yuan , Z. 2000 . How good is prediction of protein structural class by the component-coupled method? . Proteins , 38 : 165 – 175 .
  • Xiao , X. , Shao , S.H. , Huang , Z.D. and Chou , K.C. 2006 . Using pseudo amino acid composition to predict protein structural classes: Approached with complexity measure factor . Journal of Computational Chemistry , 27 : 478 – 482 .
  • Xie , D. , Li , A. , Wang , M. , Fan , Z. and Feng , H. 2005 . LOCSVMPSI: A web server for subcellular localization of eukaryotic proteins using SVM and profile of PSI-BLAST . Nucleic Acids Research , 33 : W105 – W110 .
  • Yang , J.Y. , Peng , Z.L. and Chen , X. 2010 . Prediction of protein structural classes for low-homology sequences based on predicted secondary structure . BMC Bioinformatics , 11 ( Suppl. 1 ) : S9
  • Yang , J.Y. , Peng , Z.L. , Yu , Z.G. , Zhang , R.J. , Anh , V. and Wang , D.S. 2009 . Prediction of protein structural classes by recurrence quantification analysis based on chaos game representation . Journal of Theoretical Biology , 257 : 618 – 626 .
  • Yuan , Z. , Bailey , T.L. and Teasdak , R.D. 2005 . Prediction of protein B-factor profiles . Proteins , 58 : 905 – 912 .
  • Yuan , Z. and Huang , B. 2004 . Prediction of protein accessible surface areas by support vector regression . Proteins , 57 : 558 – 564 .
  • Zhang , T.L. and Ding , Y.S. 2007 . Using pseudo amino acid composition and binary-tree support vector machines to predict protein structural classes . Amino Acids , 33 : 623 – 629 .
  • Zhang , T.L. , Ding , Y.S. and Chou , K.C. 2008 . Prediction protein structural classes with pseudo-amino acid composition: Approximate entropy and hydrophobicity pattern . Journal of Theoretical Biology , 250 : 186 – 193 .
  • Zhang , S.L. , Ding , S.Y. and Wang , T.M. 2011 . High-accuracy prediction of protein structural class for low-similarity sequences based on predicted secondary structure . Biochimie , 93 : 710 – 714 .
  • Zhang , S. , Yang , L. and Wang , T. 2009 . Use of information discrepancy measure to compare protein secondary structures . Journal of Molecular Structure: THEOCHEM , 909 : 102 – 106 .
  • Zhou , G.P. 1998 . An intriguing controversy over protein structural class prediction . Journal of Protein Chemistry , 17 : 729 – 738 .

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