Prediction of caspase cleavage sites using Bayesian bio-basis function neural networks

Bioinformatics

Volumn 21, Issue 9, 2005, Pages 1831-1837

  Yang, Zheng Rong ^a  

^a UNIVERSITY OF EXETER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CASPASE;

ACCURACY; ALGORITHM; AMINO ACID SEQUENCE; APOPTOSIS; ARTICLE; ARTIFICIAL NEURAL NETWORK; BAYES THEOREM; MATHEMATICAL PARAMETERS; NONBIOLOGICAL MODEL; NORMAL DISTRIBUTION; PREDICTION; PRIORITY JOURNAL; SIMULATION;

EID: 18744369642     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti281     Document Type: Article

References (29)

1. Adams,J.M. and Cory,S. (1998) The Bcl-2 protein family: arbiters of cell survival. Science, 281, 1322-1326.
2. Berry,E. et al. (2004) Reduced bio-basis function neural networks in prediction of phosphorylation sites, a comparative study. Comput. Biol. Chem., 28, 75-85.
3. Blom,N. et al. (1999) Sequence and structure based prediction of eukaryotic protein phosphorylation sites. J. Mol. Biol., 294, 1351-1362.
4. Cai,Y.D. and Chou,K.C. (1998) Artificial neural network model for predicting HIV protease cleavage sites in protein. Advances in Engineering Software, 29, 119-128.
5. Chen,S. et al. (2003) Kernel-based nonlinear beamforming construction using orthogonal forward selection with Fisher ratio class separability measure. IEEE Signal Processing Letters, 11, 478-481.
6. Chou,K.C. et al. (2000) Prediction of the tertiary structure of a caspase-9/inhibitor complex. FEBS Lett., 470, 249-256.
7. Duda,R.O., Hart,P.E. and Stork,D.G. (2002) Pattern Classification and Scene Analysis. 2nd edn. Wiley, NY.
8. Ethell,D.W. et al. (2001) Caspase 7 can cleave tumor necrosis factor receptor-I (p6O) at a non-consensus motif, in vitro. Biochim. Biophys. Acta, 1541, 231-238.
9. Evan,G. and Littlewood,T. (1998) A matter of life and cell death. Science, 281, 1317-1322.
10. Gutteridge,A. et al. (2003) Using a neural network and spatial clustering to predict the location of active sites in enzymes. J. Mol. Biol., 330, 719-734.
11. Henikoff,S. and Henikoff,J.G. (1992) Amino acid substitution matrices from protein blocks. Proc. Natl Sci. Acad. USA, 89, 10915-10919.
12. Jakobi,R. (2004) Subcellular targeting regulates the function of caspase-activated protein kinases in apopsis. Drug Resist. Updat., 7, 11-17.
13. Joachims,T. (1999) Making large-scale SVM learning practical. In Schölkopf,B., Burges,C. and Smola,A. (eds), Advances in Kernel Methods - Support Vector Learning, MIT Press, Cambridge, MA.
14. Li,Y. et al. (2002) Bayesian automatic relevance determination algorithms for classifying gene expression data. Bioinformatics, 18, 1332-1339.
15. Nabney,I. (2003) Netlab: Algorithms for Pattern Recognition, Springer.
16. Narayanan,A. et al. (2002) Mining viral protease data to extract cleavage knowledge. Bioinformatics, 18, S5-S13.
17. Nielsen,H. et al. (1997) Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng., 10, 1-6.
18. Qian,N. and Sejnowski,T.J. (1988) Predicting the secondary structure of globular proteins using neural network models. J. Mol. Biol., 202, 865-884.
19. Reed,J.C. and Paternostro,G. (1999) Postmitochondrial regulation of apoptosis during heart failure. Proc. Natl Acad. Sci. USA, 96, 7614-7616.
20. Rohn,T.T. et al. (2004) Caspase activaion independent of cell death is required for proper cell dispersal and correct morphology in PC12 cells. Exp. Cell Res., 293, 215-225.
21. Thomson,R. et al. (2003) Characterising proteolytic cleavage site activity using bio-basis function neural networks. Bioinformatics, 19, 1741-1747, 2003.
22. Thompson,T.B. et al. (1995) Neural network prediction of the HIV-1 protease cleavage sites. J. Theor. Biol., 177, 369-379.
23. Tipping,M.E. (2000) The relevance vector machine. Adv. Neural Inf. Process. Syst., 12, 652-658.
24. Van de Craen,M. et al. (1999) Identification of caspases that cleave presenilin-1 and presenilin-2. FEBS Lett., 445, 149-154.
25. Vapnik,V. (1995) The Nature of Statistical Learning Theory. Springer-Verlag, NY.
26. West,K.A. et al. (2002) Activation of the P13K/Akt pathway and chemotherapeutic resistance. Drug Resist. Updat., 5, 234-248.
27. Wilson,R.L. and Sharda,R. (1994) Bankruptcy prediction using neural networks. Decision Support Systems, 11, 545-557.
28. Yang,Z.R. and Chou,K.C. (2003) Mining biological data using Self-organising Map. J. Chem. Inf. Comput. Sci., 43, 1748-1753.
29. Yang,Z.R. and Chou,K.C. (2004) Bio-basis function neural networks for the prediction of the O-linkage sites in glyco-proteins. Bioinformatics, 20, 903-908.