Predicting caspase substrate cleavage sites based on a hybrid SVM-PSSM method

Protein and Peptide Letters

Volumn 17, Issue 12, 2010, Pages 1566-1571

  Li, Dandan ^a   Jiang, Zhenran ^a   Yu, Weiming ^a   Du, Lei ^b  

^a EAST CHINA NORMAL UNIVERSITY   (China)

^b China Petroleum Engineering Southwest Company   (China)

Author keywords

Caspase; PSSM profiles; Substrate cleavage sites prediction; SVM

Indexed keywords

EID: 78650652567     PISSN: 09298665     EISSN: None     Source Type: Journal    
DOI: 10.2174/0929866511009011566     Document Type: Article

References (72)

1. Gagliardini, V.; Fernandez, P.A.; Lee, R.K.K.; Drexler, H.C.A.; Rotello, R.J.; Fishman, M.C.; Yuan, J. Prevention of vertebrate neuronal death by the crmA gene. Science, 1994, 263, 826-828.
2. Launary, S.; Hermine, O.; Fontenay, M.; Kroemer, G.; Solary, E. Vital functions for lethal caspases. Oncogene, 2005, 24, 5137-5148.
3. Timmer, J.C.; Salvesen, G.S. Caspase substrate. Cell Death Differ., 2007, 14, 66-72.
4. Graf, D.; Bode, J.G.; Häussinger, D. Caspases and receptor cleavage. Arch. Biochem. Biophys., 2007, 462, 162-170.
5. Chou, K.C. A vectorized sequence-coupling model for predicting HIV protease cleavage sites in proteins. J. Biol. Chem., 1993, 268, 16938-16948.
6. Thompson, T.B.; Chou, K.C.; Zheng, C. Neural network prediction of the HIV-1 protease cleavage sites. J. Theor. Biol., 1995, 177, 369-379.
7. Chou, K.C. Review: Prediction of HIV protease cleavage sites in proteins. Anal. Biochem., 1996, 233, 1-14.
8. 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.
9. Chou, K.C.; Shen, H.B. Plant-mPLoc: A Top-Down Strategy to Augment the Power for Predicting Plant Protein Subcellular Localization. PLoS One, 2010, 5, e11335.
10. Chou, K.C.; Jones, D.; Heinrikson, R.L. Prediction of the tertiary structure and substrate binding site of caspase-8. FEBS Lett., 1997, 479, 49-54.
11. Chou, J.J.; Matsuo, H.; Duan, H.; Wagner, G. Solution structure of the RAIDD CARD and model for CARD/CARD interaction in caspase-2 and caspase-9 recruitment. Cell, 1998, 94, 171-180.
12. Chou, K.C.; Tomasselli, A.G.; Heinrikson, R.L. Prediction of the Tertiary Structure of a Caspase-9/Inhibitor Complex. FEBS Lett., 2000, 470, 249-256.
13. Chou, K.C. Review: Structural bioinformatics and its impact to biomedical science. Curr. Med. Chem., 2004, 11, 2105-2134.
14. Luthi, A.U.; Martin, S.J. CASBAH: a searchable database of caspase substrate. Cell Death Differ., 2007, 14, 641-650.
15. Igarashi, Y.; Eroshkin, A.; Gramatikova, S.; Gramatikoff, G.; Zhang, Y.; Smith, J.W.; Osterman, A.L.; Godzik, A. CutDB: a proteolytic event database. Nucleic Acids Res., 2007, 35, D546-D549.
16. Yang, Z.R. Prediction of caspase cleavage sites using Bayesian bio-basis function neural networks. Bioinformatics, 2005, 27 , 1831-1837.
17. Verspurten, J.; Gevaert, K.; Declercq, W.; Vandenabeele, P. SitePredicting the cleavage of proteinase substrate. Trends Biochem Sci., 2009, 34(7), 319-323.
18. Lohmuller, T. Toward Computer-Based Cleavage Site Prediction of Cysteine Endopeptidases. Biol. Chem., 2003, 384, 899-909.
19. Backes, C. GraBCas: a bioinformatics tool for score-based prediction of Caspase-and Granzyme B cleavage sites in protein sequences. Nucleic Acids Res., 2005, 33, W208-W213.
20. Garay-Malpartida, H.M.; Occhiucci, J.M.; Alves, J.; Belizário, J.E. CasPredictior: a new computer-based tool for caspase substrate prediction. Bioinformatics, 2005, 27 , i169-i176.
21. Boyd, S.E.; PoPS: A computational tool for modeling and predicting protease specificity. J. Bioinform. Comput. Biol. , 2005, 3, 551-585.
22. Rawlings, N.D.; Barrett, A.J. MEROPS: the peptidase database. Nucleic Acids Res., 1999, 27, 325-331.
23. Wee, L.J.; Tan, T.W.; Ranganathan, S. SVM-based prediction of caspase substrate cleavage sites. BMC Bioinformatics, 2006, 7, S14.
24. Wee, L.J.; Tan, T.W.; Ranganathan, S. CASVM: web server for SVM-based prediction of caspase substrate cleavage sites. Bioinformatics, 2007, 23, 3241-3243.
25. Utz, P.J.; Anderson, P. Life and death decisions: regulation of apoptosis by proteolysis of signaling molecules. Cell Death Differ., 2000, 7, 589-602.
26. Los, M.; Stroh, C.; Janicke, R.U.; Engels, I.H.; Schulze-Osthoff, K. Caspases: more than just killers? Trends Immunol., 2001, 22, 31-34.
27. Yang, Z.R. Biological applications of support vector machines. Brief Bioinform., 2004, 5, 328-338.
28. Cai, Y.D.; Zhou, G.P.; Chou, K.C. Support vector machines for predicting membrane protein types by using functional domain composition. Biophys. J., 2003, 84, 3257-3263.
29. Cai, Y.D.; Liu, X.J.; Xu, X.B.; Chou, K.C. Prediction of protein structural classes by support vector machines. Comput. Chem., 2002, 26, 293-296.
30. Chou, K.C.; Cai, Y.D. Using functional domain composition and support vector machines for prediction of protein subcellular location. J. Biol. Chem., 2002, 277, 45765-45769.
31. Cai, Y.D.; Liu, X.J.; Xu, X.B.; Chou, K.C. Support vector machines for predicting the specificity of GalNAc-transferase. Peptides, 2002, 23, 205-208.
32. Cai, Y.D.; Liu, X.J.; Xu, X.B.; Chou, K.C. Support vector machines for predicting HIV protease cleavage sites in protein. J. Comput. Chem., 2002, 23, 267-274.
33. Cai, Y.D.; Liu, X.J.; Xu, X.B.; Chou, K.C. Support vector machines for the classification and prediction of beta-turn types. J. Pept Sci., 2002, 8, 297-301.
34. Cai, Y.D.; Lin, S.; Chou, K.C. Support vector machines for prediction of protein signal sequences and their cleavage sites. Peptides, 2003, 24, 159-161.
35. Cai, Y.D.; Feng, K. Y.; Li, Y.X.; Chou, K.C. Support vector machine for predicting alpha-turn types. Peptides, 2003, 24, 629-630.
36. Cai, Y.D.; Zhou, G.P.; Jen, C.H.; Lin, S.L.; Chou, K.C. Identify catalytic triads of serine hydrolases by support vector machines. J. Theor. Biol., 2004, 228, 551-557.
37. 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.
38. Chang, C.C.; Lin, C.J. (2001) LIBSVM: a library for support vector machines. (openly accessible at http://www.csie.ntu.edu.tw/~cjlin/libsvm/)
39. Altschul, S.F.; Madden, T.L.; Schaffer, A.A.; Zhang, J.H.; Zhang, Z.; Miller, W.; Lipman, D.J. Grapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 1997, 25, 3389-3403.
40. Kim, H. Protein secondary structure prediction based on an improved support vector machines approach. Protein Eng., 2003, 16, 553-560.
41. Ho, S.Y. Design of accurate predictors for DNA-binding sites in proteins using hybrid SVM-PSSM method. BioSystems, 2006, 90, 234-241.
42. Kumar, M. Prediction of RNA binding sites in a protein using SVM and PSSM profile. Proteins, 2007, 71, 189-194.
43. Zimmermann, O.; Hansmann, U.H.E. Support vector machines for prediction of dihedral angle regions. Bioinformatics, 2006, 22, 3009-3015.
44. He, J.; Hu, H.J.; Harrison, R.; Tai, P.C.; Pan, Y. Transmembrane segments prediction and understanding using support vector machine and decision tree. Expert Syst. Appl., 2006, 30, 64-72.
45. 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.
46. 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.
47. Shen, H.B.; Chou, K.C. EzyPred: A top-down approach for predicting enzyme functional classes and subclasses. Biochem. Biophys. Res. Comm., 2007, 364, 53-59.
48. Shen, H.B.; Chou, K.C. Predicting protein fold pattern with functional domain and sequential evolution information. J. Theor. Biol., 2009, 256, 441-446.
49. Henikoff, S.; Henikoff, J.G. Amino acid substitution matrices from protein blocks. Biochemistry, 1992, 89, 10915-10919.
50. Jones, D.T. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol., 1999, 292, 195-202.
51. Chou, K.C.; Zhang, C.T. Review: Prediction of protein structural classes. Crit. Rev. Biochem. Mol. Biol., 1995, 30, 275-349.
52. Chou, K.C.; Shen, H.B. Cell-PLoc: A package of Web servers for predicting subcellular localization of proteins in various organisms. Nat. Protoc., 2008, 3, 153-162.
53. Chou, K.C.; Shen, H.B. Review: Recent progresses in protein subcellular location prediction. Anal. Biochem., 2007, 370, 1-16.
54. Zhou, G.P. An intriguing controversy over protein structural class prediction. J. Protein Chem., 1998, 17, 729-738.
55. Zhou, X.B.; Chen, C.; Li, Z.C.; Zou, X.Y. Using Chou's amphiphilic pseudo-amino acid composition and support vector machine for prediction of enzyme subfamily classes. J. Theor. Biol., 2007, 248, 546-551.
56. Lin, H. The modified Mahalanobis discriminant for predicting outer membrane proteins by using Chou's pseudo amino acid composition. J. Theor. Biol., 2008, 252, 350-356.
57. Jiang, X.; Wei, R.; Zhang, T. L.; Gu, Q. Using the concept of Chou's pseudo amino acid composition to predict apoptosis proteins subcellular location: an approach by approximate entropy. Protein Pept. Lett., 2008, 15, 392-396.
58. Li, F.M.; Li, Q.Z. Predicting protein subcellular location using Chou's pseudo amino acid composition and improved hybrid approach. Protein Pept. Lett., 2008, 15, 612-616.
59. Lin, H.; Ding, H.; Guo, F.B.; Zhang, A.Y.; Huang, J. Predicting subcellular localization of mycobacterial proteins by using Chou's pseudo amino acid composition. Protein Pept. Lett., 2008, 15, 739-744.
60. Ding, Y.S.; Zhang, T.L. Using Chou's pseudo amino acid composition to predict subcellular localization of apoptosis proteins: an approach with immune genetic algorithm-based ensemble classifier. Pattern Recognition Letters, 2008, 29, 1887-1892.
61. 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. Protein Pept. Lett., 2009, 16, 27-31
62. Ding, H.; Luo, L.; Lin, H. Prediction of cell wall lytic enzymes using Chou's amphiphilic pseudo amino acid composition. Protein Pept. Lett., 2009, 16, 351-355.
63. 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.
64. Qiu, J.D.; Huang, J.H.; Liang, R.P.; Lu, X.Q. Prediction of G-protein-coupled receptor classes based on the concept of Chou's pseudo amino acid composition: an approach from discrete wavelet transform. Anal Biochem., 2009, 390, 68-73.
65. 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., 2009, 2, 136-143 http://www.srpublishing. org/journal/jbise/ (Accessed September 5, 2010).
66. Chou, K.C.; Shen, H.B. FoldRate: A web-server for predicting protein folding rates from primary sequence. The Open Bioinformatics Journal, 2009, 3, 31-50 http://www.bentham.org/ open/tobioij/ (Accessed September 5, 2010).
67. Chou, K.C.; Shen, H.B. Euk-mPLoc: a fusion classifier for large-scale eukaryotic protein subcellular location prediction by incorporating multiple sites. J. Proteome Res., 2007, 6, 1728-1734.
68. 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.
69. 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.
70. Park, S.H.; Goo, J.M.; Jo, C.H. Receiver Operating Characteristic (ROC) curve practical review for radiologists. Korean J. Radiol., 2004, 5, 11-18.
71. Fischer, U.; Janicke, R.U., Schulze-Osthoff, K. Many cuts to ruin: a comprehensive update of caspase substrate. Cell Death Differ., 2003, 10, 76-100.
72. Chou, K.C.; Shen, H.B. Review: recent advances in developing web-servers for predicting protein attributes. Natural Science, 2009, 2, 63-92. http://www.scirp.org/journal/NS/ (Accessed September 5, 2010).