Geometry preserving projections algorithm for predicting membrane protein types

Journal of Theoretical Biology

Volumn 262, Issue 2, 2010, Pages 208-213

  Wang, Tong ^a   Xia, Tian ^a   Hu, Xiao ming ^a  

^a SHANGHAI SECOND POLYTECHNIC UNIVERSITY   (China)

Author keywords

Bioinformatics; Dimensionality reduction; K nearest neighbor (K NN)

Indexed keywords

MEMBRANE PROTEIN;

ALGORITHM; BIOINFORMATICS; GEOMETRY; MATRIX; MEMBRANE; PEPTIDE; PREDICTION; PROTEIN; REDUCTION; VECTOR;

AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; CLASSIFICATION ALGORITHM; GEOMETRY; JACKKNIFE TEST; K NEAREST NEIGHBOR; PREDICTION; PRIORITY JOURNAL; SUPPORT VECTOR MACHINE;

ALGORITHMS; DATABASES, PROTEIN; MEMBRANE PROTEINS; SEQUENCE ANALYSIS, PROTEIN;

EID: 70450253187     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2009.09.027     Document Type: Article

References (28)

1. Bhasin M., and Raghava G.P. ESLpred: SVM-based method for subcellular localization of eukaryotic proteins using dipeptide composition and PSI-BLAST. Nucleic Acids Res. 32 (2004) W414-W419
2. Bhasin M., and Raghava G.P. GPCRpred: an SVM-based method for prediction of families and subfamilies of G-protein coupled receptors. Nucleic Acids Res. 32 (2004) W383-W389
3. Bhasin M., and Raghava G.P. GPCRsclass: a web tool for the classification of amine type of G-protein-coupled receptors. Nucleic Acids Res. 33 (2005) W143-W147
4. Chen J., Liu H., Yang J., and Chou K.C. Prediction of linear B-cell epitopes using amino acid pair antigenicity scale. Amino Acids 33 (2007) 423-428
5. Chou K.C. A novel approach to predicting protein structural classes in a (20-1)-D amino acid composition space. Proteins 21 (1995) 319-344
6. Chou K.C. Prediction of protein cellular attributes using pseudo-amino acid composition. Proteins 43 (2001) 246-255
7. Chou K.C. Structural bioinformatics and its impact to biomedical science. Curr. Med. Chem. 11 (2004) 2105-2134
8. Chou K.C. Insights from modeling three-dimensional structures of the human potassium and sodium channels. J. Proteome. Res. 3 (2004) 856-861
9. Chou K.C., and Elrod D.W. Prediction of membrane protein types and subcellular locations. Proteins 34 (1999) 137-153
10. Chou K.C., and Shen H.B. MemType-2L: a web server for predicting membrane proteins and their types by incorporating evolution information through Pse-PSSM. Biochem. Biophys. Res. Commun. 360 (2007) 339-345
11. Denoeux T. A k-nearest neighbor classification rule based on Dempster-ShaferTheory. IEEE. Trans. Syst. Man Cybern. 25 (1995) 804-813
12. Douglas S.M., Chou J.J., and Shih W.M. DNA-nanotube-induced alignment of membrane proteins for NMR structure determination. Proc. Natl. Acad. Sci. USA 104 (2007) 6644-6648
13. Grassmann J., Reczko M., Suhai S., and Edler L. Protein fold class prediction: new methods of statistical classification. Proc. Int. Conf. Intell. Syst. Mol. Biol. (1999) 106-112
14. Huang Y., and Li Y. Prediction of protein subcellular locations using fuzzy k-NN method. Bioinformatics 20 (2004) 21-28
15. Keller J.M., and Gray M.R. A fuzzy k-nearest neighbor algorithm. IEEE Trans. Syst. Man Cybern. 15 (1985) 580-585
16. Liu D.Q., Liu H., Shen H.B., Yang J., and Chou K.C. Predicting secretory protein signal sequence cleavage sites by fusing the marks of global alignments. Amino Acids 32 (2007) 493-496
17. Nakashima H., Nishikawa K., and Ooi T. The folding type of a protein is relevant to the amino acid composition. J. Biochem. 99 (1986) 153-162
18. Nanni L., and Lumini A. An ensemble of support vector machines for predicting the membrane protein type directly from the amino acid sequence. Amino Acids 35 (2008) 573-580
19. Nanni L., and Lumini A. Genetic programming for creating Chou's pseudo amino acid based features for submitochondria localization. Amino Acids 34 (2008) 653-660
20. Niu B., Cai Y.D., Lu W.C., Li G.Z., and Chou K.C. Predicting protein structural class with AdaBoost Learner. Protein Pept. Lett. 13 (2006) 489-492
21. Reczko M., and Bohr H. The DEF data base of sequence based protein fold class predictions. Nucleic Acids Res. 22 (1994) 3616-3619
22. Schaffer A.A., Aravind L., Madden T.L., Shavirin S., Spouge J.L., Wolf Y.I., Koonin E.V., and Altschul S.F. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res. 29 (2001) 2994-3005
23. Schnell J.R., and Chou J.J. Structure and mechanism of the M2 proton channel of influenza A virus. Nature 451 (2008) 591-595
24. Shen H.B., and Chou K.C. Nuc-PLoc: a new web-server for predicting protein subnuclear localization by fusing PseAA composition and PsePSSM. Protein Eng. Des. Sel. 20 (2007) 561-567
25. Spiess M. Heads or tails-what determines the orientation of proteins in the membrane. FEBS Lett. 369 (1995) 76-79
26. Wang M., Yang J., and Chou K.C. Using string kernel to predict signal peptide cleavage site based on subsite coupling model. Amino Acids 28 (2005) 395-402
27. Xiao X., Shao S., Ding Y., Huang Z., Huang Y., and Chou K.C. Using complexity measure factor to predict protein subcellular location. Amino Acids 28 (2005) 57-61
28. Zhang T.H., Li X.L., Tao D.C., and Yang J. Multimodal biometrics using geometry preserving projections. Pattern Recognition 41 (2008) 805-813