Exploring potential discriminatory information embedded in PSSM to enhance protein structural class prediction accuracy

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 7986 LNBI, Issue , 2013, Pages 208-219

  Dehzangi, Abdollah ^a,b   Paliwal, Kuldip ^a   Lyons, James ^a   Sharma, Alok ^c   Sattar, Abdul ^a,b  

^a GRIFFITH UNIVERSITY   (Australia)

^b CSIRO   (Australia)

^c UNIVERSITY OF THE SOUTH PACIFIC   (Fiji)

Author keywords

Feature Extraction; Protein Structural Class Prediction Problem; Segmented Auto Covariance; Segmented distribution; Support Vector Machine (SVM)

Indexed keywords

BIOINFORMATICS; DISCRIMINATORS; EXTRACTION; FEATURE EXTRACTION; PROTEINS; SUPPORT VECTOR MACHINES;

AUTOCOVARIANCES; FEATURE EXTRACTION TECHNIQUES; POSITION SPECIFIC SCORING MATRIX; PREDICTION ACCURACY; SEGMENTED DISTRIBUTION; STRUCTURAL CLASS; TERTIARY STRUCTURES;

FORECASTING;

EID: 84880723300     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-39159-0_19     Document Type: Conference Paper

References (31)

1. Chothia, C.: The nature of the accessible and buried surfaces in proteins. Journal of Molecular Biology 105(1), 1-12 (1976)
2. Chou, K.C.: Progress in protein structural class prediction and its impact to bioinformatics and proteomics. Current Protein and Peptide Science 6, 423-436 (2005)
3. Wang, Z.X., Yuan, Z.: How good is prediction of protein structural class by the component-coupled method? Proteins: Structure, Function, and Bioinformatics 38(2), 165-175 (2000)
4. Chou, K.C.: Some remarks on protein attribute prediction and pseudo amino acid composition. Journal of Theoretical Biology 273(1), 236-247 (2011)
5. Yang, J.Y., Peng, Z.L., Chen, X.: Prediction of protein structural classes for lowhomology sequences based on predicted secondary structure. BMC Bioinformatics 11(suppl. 1), S9 (2010)
6. Li, Z.C., Zhou, X.B., Lin, Y.R., Zou, X.Y.: Prediction of protein structure class by coupling improved genetic algorithm and support vector machine. Amino Acids 35(3), 581-590 (2008)
7. Zhang, S., Ding, S., Wang, T.: High-accuracy prediction of protein structural class for low-similarity sequences based on predicted secondary structure. Biochimie 93(4), 710-714 (2011)
8. Liu, T., Jia, C.: A high-accuracy protein structural class prediction algorithm using predicted secondary structural information. Journal of Theoretical Biology 267(3), 272-275 (2010)
9. Jahandideh, S., Abdolmaleki, P., Jahandideh, M., Asadabadi, E.B.: Novel twostage hybrid neural discriminant model for predicting proteins structural classes. Biophysical Chemistry 128(1), 87-93 (2007)
10. Jahandideh, S., Abdolmaleki, P., Jahandideh, M., Hayatshahi, S.H.S.: Novel hybrid method for the evaluation of parameters contributing in determination of protein structural classes. Journal of Theoretical Biology 244(2), 275-281 (2007)
11. Cai, Y.D., Feng, K., Lu, W., Chou, K.: Using logitboost classifier to predict protein structural classes. Theoretical Biollogy 238, 172-176 (2006)
12. Jain, P., Hirst, J.: Automatic structure classification of small proteins using random forest. BMC Bioinformatics 11(1), 364 (2010)
13. Kurgan, L.A., Chen, K.: Prediction of protein structural class for the twilight zone sequences. Biochemical and Biophysical Research Communications 357(2), 453-460 (2007)
14. Kurgan, L.A., Zhang, T., Zhang, H., Shen, S., Ruan, J.: Secondary structure-based assignment of the protein structural classes. Amino Acids 35, 551-564 (2008)
15. Chen, K., Kurgan, L.A., Ruan, J.: Prediction of protein structural class using novel evolutionary collocation-based sequence representation. Journal of Computational Chemistry 29(10), 1596-1604 (2008)
16. Mizianty, M., Kurgan, L.A.: Modular prediction of protein structural classes from sequences of twilight-zone identity with predicting sequences. BMC Bioinformatics 10(1), 414 (2009)
17. Liu, T., Geng, X., Zheng, X., Li, R., Wang, J.: Accurate prediction of protein structural class using auto covariance transformation of psi-blast profiles. Amino Acids 42, 2243-2249 (2012)
18. Zhang, S., Ye, F., Yuan, X.: Using principal component analysis and support vector machine to predict protein structural class for low-similarity sequences via pssm. Journal of Biomolecular Structure and Dynamics 29(6), 1138-1146 (2012)
19. Kurgan, L.A., Homaeian, L.: 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 (2006)
20. Yang, J.Y., Peng, Z.L., Yu, Z.G., Zhang, R.J., Anh, V., Wang, D.: Prediction of protein structural classes by recurrence quantification analysis based on chaos game representation. Journal of Theoretical Biology 257(4), 618-626 (2009)
21. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J.H., Zhang, Z., Miller, W., Lipman, D.J.: Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Research 17, 3389-3402 (1997)
22. Jones, D.T.: Protein secondary structure prediction based on position-specific scoring matrices. Journal of Molecular Biology 292(2), 195-202 (1999)
23. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E.: The protein data bank. Nucleic Acids Research 28(1), 235-242 (2000)
24. Murzin, A.G., Brenner, S.E., Hubbard, T., Chothia, C.: Scop: A structural classification of proteins database for the investigation of sequences and structures. Journal of Molecular Biology 247(4), 536-540 (1995)
25. Vapnik, V.N.: The nature of statistical learning theory. Springer-Verlag New York, Inc. (1995)
26. Chang, C.C., Lin, C.J.: Libsvm: a library for support vector machines (2001)
27. Costantini, S., Facchiano, A.M.: Prediction of the protein structural class by specific peptide frequencies. Biochimie 91(2), 226-229 (2009)
28. Kurgan, L.A., Cios, K.J., Chen, K.: Scpred: Accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences. BMC Bioinformatics 9, 226 (2008)
29. Li, Z.C., Zhou, X.B., Dai, Z., Zou, X.Y.: 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 (2009)
30. Zhang, T.L., Ding, Y.S., Chou, K.C.: Prediction protein structural classes with pseudo amino acid composition: approximate entropy and hydrophobicity pattern. Theoretical Biology 250, 186-193 (2008)
31. Chen, C., Zhou, X., Tian, Y., Zou, X., Cai, P.: Predicting protein structural class with pseudo-amino acid composition and support vector machine fusion network. Analytical Biochemistry 357(1), 116-121 (2006)