Prediction of protein structural classes for low-homology sequences based on predicted secondary structure

BMC Bioinformatics

Volumn 11, Issue SUPPLL.1, 2010, Pages

  Yang, Jian Yi ^a   Peng, Zhen Ling ^b   Chen, Xin ^a  

^a NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

^b GUIZHOU UNIVERSITY OF ENGINEERING SCIENCE   (China)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; CHAOS GAME REPRESENTATION; FISHER'S DISCRIMINANT; INFORMATION ENTROPY; PREDICTION ACCURACY; RECURRENCE QUANTIFICATION ANALYSIS; SECONDARY STRUCTURAL ELEMENTS; SECONDARY STRUCTURES;

AMINO ACIDS; PROTEINS; BIOINFORMATICS;

FORECASTING;

PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CLASSIFICATION; ENTROPY; MOLECULAR GENETICS; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; SEQUENCE HOMOLOGY;

ALGORITHMS; AMINO ACID SEQUENCE; ENTROPY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 76649141763     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-S1-S9     Document Type: Article

References (42)

1. Anfinsen C. Principles that govern the folding of protein chains. Science 1973, 181:223-230. 10.1126/science.181.4096.223, 4124164.
2. Levitt M, Chothia C. Structural patterns in globular proteins. Nature 1976, 261:552-558. 10.1038/261552a0, 934293.
3. Bahar I, Atilgan AR, Jernigan RL, Erman B. Understanding the recognition of protein structural classes by amino acid composition. Proteins 1997, 29:172-185. 10.1002/(SICI)1097-0134(199710)29:2<172::AID-PROT5>3.0.CO;2-F, 9329082.
4. Chou KC, Zhang CT. Predicting of protein structural class. Crit Rev Biochem Mol Biol 1995, 30:275-349. 10.3109/10409239509083488, 7587280.
5. Kedarisetti KD, Kurgan LA, Dick S. Classifier ensembles for protein structural class prediction with varying homology. Biochem Biophys Res Commun 2006, 348:981-988. 10.1016/j.bbrc.2006.07.141, 16904630.
6. Kurgan LA, 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 Recogn 2006, 39:2323-2343.
7. Wang ZX, Yuan Z. How good is the prediction of protein structural class by the component-coupled method?. Pattern Recogn 2000, 38:165-175.
8. Chou KC. A novel approach to predicting protein structural classes in a (20-1)-D amino acid composition space. Proteins 1995, 21:319-344. 10.1002/prot.340210406, 7567954.
9. Chou KC, Liu WM, Maggiora GM, Zhang CT. Prediction and classification of domain structural classes. Proteins 1998, 31:97-130. 10.1002/(SICI)1097-0134(19980401)31:1<97::AID-PROT8>3.0.CO;2-E, 9552161.
10. Shen HB, Yang J, Liu XJ, Chou KC. Using supervised fuzzy clustering to predict protein structural classes. Biochem Biophys Res Commun 2005, 334:577-581. 10.1016/j.bbrc.2005.06.128, 16023077.
11. Chou KC, Maggiora GM. Domain structural class prediction. Protein Eng 1998, 11:523-538. 10.1093/protein/11.7.523, 9740370.
12. Chou KC. Prediction of protein cellular attributes using pseudo amino acid composition. Proteins 2001, 43:246-255. 10.1002/prot.1035, 11288174.
13. Chen C, Tian YX, Zou XY, Cai PX, Mo JY. Using pseudo-amino acid composition and support vector machine to predict protein structural class. J Theor Biol 2006, 243:444-448. 10.1016/j.jtbi.2006.06.025, 16908032.
14. Zhang TL, Ding YS, Chou KC. Prediction protein structural classes with pseudo-amino acid composition: Approximate entropy and hydrophobicity pattern. J Theor Biol 2008, 250:186-193. 10.1016/j.jtbi.2007.09.014, 17959199.
15. Kurgan L, Chen K. Prediction of protein structural class for the twilight zone sequences. Biochem Biophys Res Commun 2007, 357:453-460. 10.1016/j.bbrc.2007.03.164, 17433260.
16. Kurgan L, Cios K, Chen K. SCPRED: Accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences. BMC Bioinformatics 2008, 9:226. 2391167, 18452616, 10.1186/1471-2105-9-226.
17. Yang JY, Peng ZL, Yu ZG, Zhang RJ, Anh V, Wang D. Prediction of protein structural classes by recurrence quantification analysis based on chaos game representation. J Theor Biol 2009, 257:618-626. 10.1016/j.jtbi.2008.12.027, 19183559.
18. Qi J, Wang B, Hao BL. Whole proteome prokaryote phylogeny without sequence alignment: a K-String composition approach. J Mol Evol 2004, 58:1-11. 10.1007/s00239-003-2493-7, 14743310.
19. Duda RO, Hart PE, Stork DG. Pattern Classification 2001, New York: John Wiley & Sons.
20. RKS-PPSC web server. , http://www1.spms.ntu.edu.sg/~chenxin/RKS_PPSC/
21. Chen K, Kurgan LA, Ruan J. Prediction of protein structural class using novel evolutionary collocation-based sequence representation. J Comput Chem 2008, 29:1596-1604. 10.1002/jcc.20918, 18293306.
22. Costantini S, Facchiano AM. Prediction of the protein structural class by specific peptide frequencies. Biochimie 2009, 91:226-229. 10.1016/j.biochi.2008.09.005, 18957316.
23. Anand A, Pugalenthi G, Suganthan PN. Predicting protein structural class by SVM with class-wise optimized features and decision probabilities. J Theor Biol 2008, 253:375-380. 10.1016/j.jtbi.2008.02.031, 18423492.
24. Zhang ZD, Sun ZR, Zhang CT. A new approach to predict the helix/strand content of globular proteins. J Theor Biol 2001, 208:65-78. 10.1006/jtbi.2000.2201, 11162053.
25. Birzele F, Kramer S. A new representation for protein secondary structure prediction based on frequent patterns. Bioinformatics 2006, 22:2628-2634. 10.1093/bioinformatics/btl453, 16940325.
26. RCSB Protein Data Bank. , http://www.rcsb.org/pdb/home/home.do
27. SCEC Server. , http://biomine.ece.ualberta.ca
28. Murzin A, Brenner S, Hubbard T, Chothia C. SCOP: a structural classification of protein database for the investigation of sequence and structures. J Mol Biol 1995, 357:536-540.
29. SCPRED Data. , http://biomine.ece.ualberta.ca/SCPRED/SCPRED.htm
30. Jones DT. Protein secondary structure prediction based on position specific scoring matrices. J Mol Biol 1999, 292:195-202. 10.1006/jmbi.1999.3091, 10493868.
31. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402. 146917, 9254694, 10.1093/nar/25.17.3389.
32. PSIPRED 2.6 web server. , http://bioinf.cs.ucl.ac.uk/psipred/
33. Lin HN, Chang JM, Wu KP, Sung TY, Hsu WL. HYPROSP II-A knowledge-based hybrid method for protein secondary structure prediction based on local prediction confidence. Bioinformatics 2005, 21:3227-3233. 10.1093/bioinformatics/bti524, 15932901.
34. Aydin Z, Altunbasak Y, Borodovsky M. Protein secondary structure prediction for a single-sequence using hidden semi-Markov models. BMC Bioinformatics 2006, 7:118. 1434774, 16524470, 10.1186/1471-2105-7-178.
35. Duan M, Huang M, Ma C, Li L, Zhou Y. Position-specific residue preference features around the ends of helices and strands and a novel strategy for the prediction of secondary structures. Protein Sci 2008, 17:1505-1512. 2525534, 18519808, 10.1110/ps.035691.108.
36. Jeffrey HJ. Chaos game representation of gene structure. Nucleic Acids Res 1990, 18:2163-2170. 330698, 2336393, 10.1093/nar/18.8.2163.
37. Fiser A, Tusnády GE, Simon I. Chaos game representation of protein structures. J Mol Graph 1994, 12:302-304. 10.1016/0263-7855(94)80109-6, 7696222.
38. Yu ZG, Anh V, Lau KS. Chaos game representation of protein sequences based on the detailed HP model and their multifractal and correlation analyses. J Theor Biol 2004, 226:341-348. 10.1016/j.jtbi.2003.09.009, 14643648.
39. Eckmann JP, Kamphorst SO, Ruelle D. Recurrence plots of dynamical systems. Europhys Lett 1987, 4:973-977.
40. Riley MA, Van Orden GC. Tutorials in contemporary nonlinear methods for the behavioral sciences, Retrieved March 1, 2005, from http://www.nsf.gov/sbe/bcs/pac/nmbs/nmbs.jsp.
41. Zbilut JP, Webber CLJ. Embeddings and delays as derived from quantification of recurrence plots. Phys Lett A 1992, 171:199-203.
42. Webber CLJ, Zbilut JP. Dynamical assessment of physiological systems and states using recurrence plot strategies. J Appl Physiol 1994, 76:965-973.