Characteristic peptides of protein secondary structural motifs

Protein and Peptide Letters

Volumn 17, Issue 10, 2010, Pages 1198-1206

  Joshi, Rajani R ^a   Sekharan, Sheeba ^a  

^a INDIAN INSTITUTE OF TECHNOLOGY BOMBAY   (India)

Author keywords

I sites library; Peptides; Position specific probability; Probabilistic characterization; Protein secondary structure; Sequential motifs

Indexed keywords

PEPTIDE;

AMINO ACID SEQUENCE; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; GENETICS; MOLECULAR GENETICS; PROTEIN MOTIF; PROTEIN SECONDARY STRUCTURE;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; COMPUTER SIMULATION; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDES; PROTEIN STRUCTURE, SECONDARY;

EID: 77958505121     PISSN: 09298665     EISSN: None     Source Type: Journal    
DOI: 10.2174/092986610792231500     Document Type: Article

References (80)

1. Chou, K. C. A novel approach to predicting protein structural classes in a (20-1)-D amino acid composition space. Proteins: Struct., Funct., Genet., 1995, 21, 319-344.
2. Chou, K. C.; Zhang, C. T. Review: Prediction of protein structural classes. Crit. Rev. Biochem. Mol. Biol., 1995, 30, 275-349.
3. Chou, K. C. Prediction and classification of alpha-turn types. Biopolymers, 1997, 42, 837-853.
4. Chou, K. C. Review: Prediction of tight turns and their types in proteins. Anal. Biochem., 2000, 286, 1-16.
5. Chou, K. C.; Cai, Y. D. Predicting protein quaternary structure by pseudo amino acid composition. Proteins Struct. Funct. Genet., 2003, 53, 282-289.
6. Xiao, X.; Wang, P.; Chou, K. C. Quat-2L: a web-server for predicting protein quaternary structural attributes. Mol. Diver., 2010, DOI 10.1007/s11030-11010-19227-11038.
7. Xiao, X.; Wang, P.; Chou, K. C. Predicting protein quaternary structural attribute by hybridizing functional domain composition and pseudo amino acid composition J. Appl. Crystallogr., 2009, 42, 169-173.
8. Chou, K. C.; Shen, H. B. FoldRate: A web-server for predicting protein folding rates from primary sequence. The Open Bioinf. J., 2009, 3, 31-50. (openly accessible at http://www.bentham.org/open/tobioij/).
9. Shen, H. B.; Song, J. N.; Chou, K. C. Prediction of protein folding rates from primary sequence by fusing multiple sequential features. J. Biomed. Sci. Eng. (JBiSE), 2009, 2, 136-143. (openly accessible at http://www.srpublishing.org/journal/jbise/).
10. Huang, R. B.; Du, Q. S.; Wang, C. H.; Liao, S. M.; Chou, K. C. A fast and accurate method for predicting pKa of residues in proteins. Protein Eng. Des. Sel., 2010, 23, 35-42.
11. Chou, K. C. A vectorized sequence-coupling model for predicting HIV protease cleavage sites in proteins. J. Biol. Chem., 1993, 268, 16938-16948.
12. Chou, K. C. Review: Prediction of HIV protease cleavage sites in proteins. Anal. Biochem., 1996, 233, 1-14.
13. Chou, K. C.; Shen, H B.; Signal-CF: a subsite-coupled and window-fusing approach for predicting signal peptides Biochem Biophys Res Comm, 2007, 357, 633-640.
14. Chou, K. C.; Shen, H. B. Review: Recent progresses in protein subcellular location prediction. Anal. Biochem., 2007, 370, 1-16.
15. Chou, K. C.; Shen, H. B. Cell-PLoc: A package of web servers for predicting subcellular localization of proteins in various organisms. Nature Protocols, 2008, 3, 153-162.
16. Chou, K. C.; Shen, H. B. A new method for predicting the subcellular localization of eukaryotic proteins with both single and multiple sites: Euk-mPLoc 2.0 PLoS ONE, 2010, 5, e9931.
17. He, Z. S.; Zhang, J.; Shi, X. H.; Hu, L. L.; Kong, X. G.; Cai, Y. D.; Chou, K. C. Predicting drug-target interaction networks based on functional groups and biological features. PLoS ONE, 2010, 5, e9603.
18. Chou, K. C.; Elrod, D. W. Prediction of membrane protein types and subcellular locations. Proteins: Struct., Funct., Genet., 1999, 34, 137-153.
19. Chou, K. C.; 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. Comm., 2007, 360, 339-345.
20. Chou, K. C. Prediction of G-protein-coupled receptor classes. J. Proteom. Res., 2005, 4, 1413-1418.
21. Xiao, X.; Wang, P.; Chou, K. C. GPCR-CA: A cellular automaton image approach for predicting G-protein-coupled receptor functional classes. J. Comput. Chem., 2009, 30, 1414-1423.
22. Lin, W. Z.; Xiao, X.; Chou, K. C. GPCR-GIA: a web-server for identifying G-protein coupled receptors and their families with grey incidence analysis. Protein Eng. Des. Sel., 2009, 22, 699-705.
23. Chou, K. C.; Shen, H. B. ProtIdent: A web server for identifying proteases and their types by fusing functional domain and sequential evolution information. Biochem. Biophys. Res. Comm., 2008, 376, 321-325.
24. Chou, K. C. Review: Structural bioinformatics and its impact to biomedical science. Curr. Med. Chem., 2004, 11, 2105-2134.
25. Chou, K. C.; Shen, H. B. Review: recent advances in developing web-servers for predicting protein attributes. Natur. Sci., 2009, 2, 63-92. (openly accessible at http://www.scirp.org/journal/NS/).
26. Joshi, R.R.; Jyothish, N.T. e-PROPAINOR - A Web-Server for Fast Prediciton of Structure & Likely Funcitonal Sites of a Protein Sequence. Open Bioinform. J., 2010, 4, 11-16. (openly accessible at http://www.bentham.org/open/tobioij/)
27. Chou, K. C. Using pair-coupled amino acid composition to predict protein secondary structure content. J. Protein Chem., 1999, 18, 473-480.
28. Liu, W.; Chou, K. C. Protein secondary structural content prediction. Protein Eng., 1999, 12, 1041-1050.
29. Chou, K. C. Review: Structural bioinformatics and its impact to biomedical science. Curr. Med. Chem., 2004, 11, 2105-2134.
30. Shen, H. B.; Chou, K. C. HIVcleave: a web-server for predicting HIV protease cleavage sites in proteins. Anal. Biochem., 2008, 375, 388-390.
31. Chou, K. C.; Wei, D. Q.; Du, Q. S.; Sirois, S.; Zhong, W. Z. Review: Progress in computational approach to drug development against SARS. Curr. Med. Chem., 2006, 13, 3263-3270.
32. Chou, K. C. Energy-optimized structure of antifreeze protein and its binding mechanism. J. Mol. Biol., 1992, 223, 509-517.
33. Schnell, J. R.; Chou, J. J. Structure and mechanism of the M2 proton channel of influenza A virus. Nature, 2008, 451, 591-595.
34. Huang, R. B.; Du, Q. S.; Wang, C. H.; Chou, K. C. An in-depth analysis of the biological functional studies based on the NMR M2 channel structure of influenza A virus. Biochem. Biophys. Res. Comm., 2008, 377, 1243-1247.
35. Pielak, R. M.; Jason R.; Schnell, J. R.; Chou, J. J. Mechanism of drug inhibition and drug resistance of influenza A M2 channel. Proc. Nat. Acad. Sci. (USA), 2009, 106, 7379-7384.
36. Du, Q. S.; Huang, R. B.; Wang, S. Q.; Chou, K.C. Designing inhibitors of M2 proton channel against H1N1 swine influenza virus PLoS ONE, 2010, 5, e9388.
37. Wang, J.; Pielak, R. M.; McClintock, M. A.; Chou, J. J. Solution structure and functional analysis of the influenza B proton channel. Nat Struct Mol Biol, 2009, 16, 1267-1271.
38. Chou, K. C. Review: Low-frequency collective motion in biomacromolecules and its biological functions. Biophys. Chem., 1988, 30, 3-48.
39. Chou, K. C. Low-frequency resonance and cooperativity of hemoglobin. Trends Biochem. Sci., 1989, 14, 212.
40. Chou K.C.; and C Zheng C., Strong electrostatic loop-helix interactions in bundle motif protein structures. Biophys J., 1992, 63(3), 682-688.
41. Bystroff, C.; Baker, D. Prediction of local structure in proteins using a library of sequence-structure motifs. J. Mol. Biol., 1998, 281, 565-77. (www.bioinfo.rpi.edu/bystrc/Isites/) (http://www.genocript.com/isites_motifs.html)
42. Dunbrack, R.L. Rotamar Libraries in the 21st century. Curr. Opin. Struct. Biol., 2002, 12, 431-440.
43. Lee J.; Kim S.; Lee J. Protein Structure Prediction Based on Fragment Assembly and Parameter Optimization. Biophys. Chem., 2005, 115, 209-214.
44. Joshi, R.R. A Decade of Computing to Traverse the Labyrinth of Protein Domains. Curr. Bioinform., 2007, 2, 113-131.
45. Helles, G. A Comparative Study of the Reported Performance of ab-initio Protein Structure Prediction Algorithms J. R. Soc. Interface, 2008, 5(21), 387-396
46. Chou, P.Y.; Fasman, G.D. Prediction of the secondary structure of proteins from their amino acid sequence. Adv. Enzymol. Relat. Areas. Mol Biol., 1978, 47, 45-147.
47. Chen H., Gu F.; Huang Z. Improved Chou-Fasman method for protein secondary structure prediction. BMC Bioinform. 2006, 7(4): S14. doi: 10.1186/1471-2105-7-S4-S14.
48. Jyothi S.; Joshi R. R. Ab-initio Computation of the 3D-Structure of Proteins by Nonparametric Statistical Methods - Medium & Short Range Distance Estimates. Sankhya, 2003, 65(3), 593-611.
49. Joshi, R. R.; Jyothi, S. Ab-initio Predicting and Reliability of Protein Structural Genomics by PROPAINOR. Comput. Biol. Chem., 2003, 27(3), 241-252.
50. Xie, J.; Kim, N.-K. Bayesian Models and Markov Chain Monte Carlo Methods for Protein Motifs with the Secondary Characteristics. J. Comput. Biol., 2005, 12(7), 950-968.
51. Hutchinson, E.G.; Thornton, J.M. PROMOTIF - A program to identify structural motifs in proteins. Protein Sci., 1996, 5, 212-220
52. Xiao, X.; Chou, K. C. Digital coding of amino acids based on hydrophobic index. Prot. Pep. Lett., 2007, 14, 871-875.
53. Ding, Y. S.; Zhang, T. L.; Chou, K. C. Prediction of protein structure classes with pseudo amino acid composition and fuzzy support vector machine network. Prot. Pep. Lett., 2007, 14, 811-815.
54. Chen, J.; Liu, H.; Yang, J.; Chou, K. C. Prediction of linear B-cell epitopes using amino acid pair antigenicity scale. Amino Acids, 2007, 33, 423-428.
55. Wang, T.; Yang, J.; Shen, H. B.; Chou, K. C. Predicting membrane protein types by the LLDA algorithm. Prot. Pep. Lett., 2008, 15, 915-921.
56. Chou, K. C.; Shen, H. B. ProtIdent: A web server for identifying proteases and their types by fusing functional domain and sequential evolution information Biochem. Biophys. Res. Comm., 2008, 376, 321-325.
57. Joshi R.R.; Hira U.; Suri D. Gibbs Sampling Shows Possibilities of B-cell Epitope Signatures. Prot. Pep. Lett., 2009, 16, 1393-1398.
58. Batencourt, M.R.; Skolnick, J. Universal Similarity Measures for Comparing Protein Structures. Biopolymers, 2001, 59, 305-309.
59. Xu D.; Xu Y.; Uberbacher, E.C. Computational Tools For Protein Modeling. Curr. Prot. Pep. Sci., 2000, 1(1), 1-4 (www.bentham.org/cpps1-1/index.htm)
60. Joshi R.R.; Manda C. Statistics of Catalytic Domain Sequences in Protein Kinases Vs Non-Kinases. Prot. Pep. Lett., 2007, 14, 518-527.
61. Jones D.T. Protein Secondary Structure Prediction based on Position Specific Scoring Matrices. J. Mol. Biol., 1999, 292, 195-202.
62. McGuffin, L.J.; Jones, D.T. The PSIPRED protein structure prediction server. Bioinformatics, 2000, 16(4), 404-5. (http://bioinfo.cs.ucl.ac.uk/psipred)
63. Chenna, R.; Sugawara, H.; Koike, T.; Lopez, R.; Gibson, T.J.; Higgins, D.G.; Thompson, J.D. Multiple Sequence Alignment with the Clustal Series of Programs. Nucl. Acid. Res., 2003, 31, 3497-3500 (http://www.ebi.ac.uk/Tools/clustalw/)
64. Altschul, S.F.; Madden, T.L.; Schäffer, A.A.; Zhang, J.; Zhang, Z.; Miller, W.; Lipman, D.J. Gapped BLAST and PSI-BLAST - A New Generation of Protein Database Search Programs. Nucl. Acid. Res., 1997, 25, 3389-3402 (http://blast.ncbi.nlm.nih.gov/Blast.cgi)
65. Murzin, A.G.; Brenner, S.E.; Hubbard, T.; Chothia, C. SCOP- a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 1995, 247, 536-540
66. Andreeva, A.; Howorth, D.; Brenner, S.E.; Hubbard, T.J.P.; Chothia, C.; Murzin, A.G. SCOP Database in 2004: Refinements Integrate Structure and Sequence Family Data. Nucl. Acid.Res., 2004, 32:D226-D229 (http://scop.berkeley.edu/data/scop.b.html)
67. Bateman, A.; Coin, L.; Durbin, R.; Finn, R.D.; Volker, H. V.; Jones, S.G.; Khanna, A.; Marshall, A.; Moxon, S.; Erik, L.; Sonnhammer, L.; Studholme, D.J.; Yeats, C.; Eddy, S.R. The Pfam Protein Families Database. Nucl. Acid. Res., 2004, 32, D138-D141 (http://pfam.sanger.ac.uk/)
68. Joshi, R.R., Gupta, V.K. Data Mining of VDJ Genes Reveals Interesting Clues. Prot. Pep. Lett., 2006, 13(6), 587-593.
69. Gelman, A.; Carlin, J.B.; Stern, H.S.; Rubin, D.B. Bayesian Data Analysis, 2nd ed; CRC Press: London, 2003.
70. Zhang, G. Y.; Fang, B. S. Predicting the cofactors of oxidoreductases based on amino acid composition distribution and Chou's amphiphilic pseudo amino acid composition. J. Theor. Biol., 2008, 253, 310-315.
71. Zeng, Y. H.; Guo, Y. Z.; Xiao, R. Q.; Yang, L.; Yu, L. Z.; Li, M. L. Using the augmented Chou's pseudo amino acid composition for predicting protein submitochondria locations based on auto covariance approach. J. Theor. Biol., 2009, 259, 366-372.
72. Li, F. M.; Li, Q. Z. Predicting protein subcellular location using Chou's pseudo amino acid composition and improved hybrid approach. Prot. Pep. Lett., 2008, 15, 612-616.
73. Lin, H.; Ding, H.; Feng-Biao Guo, F. B.; Zhang, A. Y.; Huang, J. Predicting subcellular localization of mycobacterial proteins by using Chou's pseudo amino acid composition. Prot. Pep. Lett., 2008, 15, 739-744.
74. Ding, H.; Luo, L.; Lin, H. Prediction of cell wall lytic enzymes using Chou's amphiphilic pseudo amino acid composition. Prot. Pep. Lett., 2009, 16, 351-355.
75. Chen, C.; Chen, L.; Zou, X.; Cai, P. Prediction of protein secondary structure content by using the concept of Chou's pseudo amino acid composition and support vector machine. Prot. Pept. Lett., 2009, 16, 27-31.
76. Esmaeili, M.; Mohabatkar, H.; Mohsenzadeh, S. Using the concept of Chou's pseudo amino acid composition for risk type prediction of human papillomaviruses. J. Theor. Biol., 2010, 263, 203-209.
77. Georgiou, D. N.; Karakasidis, T. E.; Nieto, J. J.; Torres, A. Use of fuzzy clustering technique and matrices to classify amino acids and its impact to Chou's pseudo amino acid composition. J. Theor. Biol., 2009, 257, 17-26.
78. Chou, K. C. Prediction of protein cellular attributes using pseudo amino acid composition. Proteins: Struct., Funct., Genet. 2001, 43, 246-255.
79. Erratum: ibid., 2001, Vol.44, 60.
80. Chou, K. C. Pseudo amino acid composition and its applications in bioinformatics, proteomics and system biology. Curr. Proteom., 2009, 6, 262-274.