Quad-PRE: A hybrid method to predict protein quaternary structure attributes

Computational and Mathematical Methods in Medicine

Volumn 2014, Issue , 2014, Pages

  Sheng, Yajun ^a   Qiu, Xingye ^a   Zhang, Chen ^a   Xu, Jun ^a   Zhang, Yanping ^a   Zheng, Wei ^a   Chen, Ke ^b  

^a NANKAI UNIVERSITY   (China)

^b TIANJIN POLYTECHNIC UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; PROTEINS; PROTEOMICS;

BIOLOGICAL PROCESS; COMPUTATIONAL BIOLOGY; EMPIRICAL EVALUATIONS; OVERALL ACCURACIES; POSITION SPECIFIC SCORING MATRIX; PROTEIN QUATERNARY STRUCTURE; SECONDARY STRUCTURES; SOLVENT ACCESSIBILITY;

FORECASTING;

AMINO ACID; PROTEIN;

ACCURACY; ARTICLE; HYBRID; POSITION WEIGHT MATRIX; PROTEIN QUATERNARY STRUCTURE; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; PROTEOMICS; AREA UNDER THE CURVE; BIOLOGY; CHEMISTRY; COMPUTER PROGRAM; HUMAN; PROCEDURES; PROTEIN DATABASE; RECEIVER OPERATING CHARACTERISTIC; REPRODUCIBILITY; SUPPORT VECTOR MACHINE;

AMINO ACIDS; AREA UNDER CURVE; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; HUMANS; PROTEIN STRUCTURE, QUATERNARY; PROTEINS; PROTEOMICS; REPRODUCIBILITY OF RESULTS; ROC CURVE; SOFTWARE; SUPPORT VECTOR MACHINES;

EID: 84902177692     PISSN: 1748670X     EISSN: 17486718     Source Type: Journal    
DOI: 10.1155/2014/715494     Document Type: Article

References (24)

1. Anfinsen C. B., Haber E., Sela M., White F. H. Jr., The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain. Proceedings of the National Academy of Sciences of the United States of America 1961 47 1309 1314 2-s2.0-67349189383
2. Garian R., Prediction of quaternary structure from primary structure. Bioinformatics 2001 17 6 551 556 2-s2.0-0034954937 (Pubitemid 32600502)
3. Zhang S.-W., Pan Q., Zhang H.-C., Zhang Y.-L., Wang H.-Y., Classification of protein quaternary structure with support vector machine. Bioinformatics 2003 19 18 2390 2396 2-s2.0-0346252360 10.1093/bioinformatics/btg331 (Pubitemid 38016638)
4. Chou K.-C., Cai Y.-D., Predicting protein quaternary structure by pseudo amino acid composition. Proteins: Structure, Function and Genetics 2003 53 2 282 289 2-s2.0-0141815538 10.1002/prot.10500 (Pubitemid 37193823)
5. Shi J. Y., Pan Q., Zhang S. W., Classification of protein homo-oligomers using amino acid composition distribution. Acta Biophysica Sinica 2006 22 1 49 55
6. Carugo O., A structural proteomics filter: prediction of the quaternary structural type of hetero-oligomeric proteins on the basis of their sequences. Journal of Applied Crystallography 2007 40 6 986 989 2-s2.0-36048959577 10.1107/S0021889807041076 (Pubitemid 350100293)
7. Levy E. D., PiQSi: protein quaternary structure investigation. Structure 2007 15 11 1364 1367 2-s2.0-35748959334 10.1016/j.str.2007.09.019 (Pubitemid 350051933)
8. Xiao X., Lin W.-Z., Application of protein grey incidence degree measure to predict protein quaternary structural types. Amino Acids 2009 37 4 741 749 2-s2.0-70349584162 10.1007/s00726-008-0212-9
9. Xiao X., Wang P., Chou K.-C., Quat-2L: a web-server for predicting protein quaternary structural attributes. Molecular Diversity 2011 15 1 149 155 2-s2.0-79953308534 10.1007/s11030-010-9227-8
10. Sun X.-Y., Shi S.-P., Qiu J.-D., Suo S.-B., Huang S.-Y., Liang R.-P., Identifying protein quaternary structural attributes by incorporating physicochemical properties into the general form of Chou's PseAAC via discrete wavelet transform. Molecular BioSystems 2012 8 3178 3184 10.1039/c2mb25280e
11. Kurgan L., Chen K., Prediction of protein structural class for the twilight zone sequences. Biochemical and Biophysical Research Communications 2007 357 2 453 460 2-s2.0-34247094836 10.1016/j.bbrc.2007.03.164 (Pubitemid 46603153)
12. Mizianty M. J., Kurgan L., Modular prediction of protein structural classes from sequences of twilight-zone identity with predicting sequences. BMC Bioinformatics 2009 10, article 414 2-s2.0-75149123557 10.1186/1471-2105-10-414
13. Zhang H., Zhang T., Gao J., Ruan J., Shen S., Kurgan L., Determination of protein folding kinetic types using sequence and predicted secondary structure and solvent accessibility. Amino acids 2012 42 1 271 283 2-s2.0-84860256769 10.1007/s00726-010-0805-y
14. Altschul S. F., Madden T. L., Schaffer A. A., Zhang J., Zhang Z., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 1997 25 17 3389 3402 (Pubitemid 27359211)
15. Bryson K., McGuffin L. J., Marsden R. L., Ward J. J., Sodhi J. S., Jones D. T., Protein structure prediction servers at University College London. Nucleic Acids Research 2005 33 2 W36 W38 2-s2.0-23144444979 10.1093/nar/gki410 (Pubitemid 44529876)
16. Huang J.-T., Cheng J.-P., Chen H., Secondary structure length as a determinant of folding rate of proteins with two- and three-state kinetics. Proteins: Structure, Function and Genetics 2007 67 1 12 17 2-s2.0-33847367710 10.1002/prot.21282 (Pubitemid 46340122)
17. Ahmad S., Gromiha M. M., Sarai A., Real value prediction of solvent accessibility from amino acid sequence. Proteins: Structure, Function and Genetics 2003 50 4 629 635 2-s2.0-0037340834 10.1002/prot.10328 (Pubitemid 36330487)
18. Hsu C.-W., Lin C.-J., A comparison of methods for multiclass support vector machines. IEEE Transactions on Neural Networks 2002 13 2 415 425 2-s2.0-0036505670 10.1109/72.991427 (Pubitemid 34475042)
19. Chen W., Feng P. M., Lin H., Chou K.-C., iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition. Nucleic Acids Research 2013 41 6, article e68 10.1093/nar/gks1450
20. Qiu W. R., Xiao X., Chou K. C., iRSpot-TNCPseAAC: identify recombination spots with trinucleotide composition and pseudo amino acid components. International Journal of Molecular Sciences 2014 15 2 1746 1766 10.3390/ijms15021746
21. Xu Y., Ding J., Wu L. Y., Chou K. C., iSNO-PseAAC: predict cysteine S-nitrosylation sites in proteins by incorporating position specific amino acid propensity into pseudo amino acid composition. PLoS ONE 2013 8 2, article e55844 10.1371/journal.pone.0055844
22. Chang C.-C., Lin C.-J., LIBSVM: a library for support vector machines. ACM Transactions on Intelligent Systems and Technology 2011 2 3, article 27 2-s2.0-79955702502 10.1145/1961189.1961199
23. Bailey T. L., Discovering sequence motifs. Methods in Molecular Biology 2007 395 271 292 2-s2.0-36549030269 10.1385/1-59745-514-8:271 (Pubitemid 350183301)
24. Xiao X., Lin W. Z., Chou K. C., Recent advances in predicting protein classification and their applications to drug development. Current Topics in Medicinal Chemistry 2013 13 10 1622 1635