A novel basis function neural network

ICONIP 2002 - Proceedings of the 9th International Conference on Neural Information Processing: Computational Intelligence for the E-Age

Volumn 1, Issue , 2002, Pages 441-446

  Thomson, R ^a   Yang, Zheng Rong ^a  

^a UNIVERSITY OF EXETER   (United Kingdom)

Author keywords

Basis neural networks; bioinformatics and Day hoff mutation matrix

Indexed keywords

ALGORITHMS; AMINO ACIDS; ARTIFICIAL INTELLIGENCE; BIOINFORMATICS; FUNCTIONS; HEAT CONDUCTION; IMAGE SEGMENTATION; INFORMATION SCIENCE; LEARNING ALGORITHMS;

BASIS FUNCTION NEURAL NETWORKS; BIO-BASIS FUNCTION NEURAL NETWORK; BIOLOGICAL FUNCTIONS; COMPUTATIONAL COSTS; NEURAL LEARNING ALGORITHMS; PREDICTION ACCURACY; RADIAL BASIS FUNCTION NEURAL NETWORKS; RADIAL BASIS FUNCTIONS;

RADIAL BASIS FUNCTION NETWORKS;

EID: 84965031014     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ICONIP.2002.1202209     Document Type: Conference Paper

References (43)

1. P. Arrigo, F. Giuliano, F. Scalia, A. Rapallo and G. Damiani, "Identification of a new motif on nucleic acid sequence data using Kohonen's self-organising map", CABIOS, vol. 7, pp. 353-357, 1991.
2. P. Ashorn, T.J. McQuade, S. Thaisrivongs, A.G. Tomasselli, W.G. Tarpley and B. Moss, "An inhibitor of the protease blocks maturation of human and simian immunodeficiency viruses and spread of infection", Proc. Natl. Acad. Sci. USA, vol. 87, pp. 7472-7476,1990.
3. A. Barrett and N.D. Rawlings, J.F. Woessner, Handbook of Proteolytic Enzymes. Academic Press, 1998
4. P. Baldi, G. Pollastri, C.A. Andersen and S. Brunak, "Matching protein beta-sheet partners by feedforward and recurrent neural networks", Proceedings of International Conference on Intelligent Systems for Molecular Biology, ISMB, vol. 8, pp. 25-36, 2000.
5. C. Bishop, Neural Networks for Pattern Recognition, Oxford Press, 1995.
6. Y.D. Cai and K.C. Chou, "Artificial neural network model for predicting HIV protease cleavage sites in protein", Advances in Engineering Software, vol. 29, pp. 119-128, 1998.
7. A. Carrillo, K.D. Stewart, H.L. Sham, D.W. Norbeck, W.E. Kohlbrenner, J.M. Leonard, D.J. Kempf and A. Molla, "In vitro selection and characterization of human immunodeficiency virus type 1 variants with increased resistance to ABT-378, a novel protease inhibitor", Journal of Virology, vol. 72, pp. 7532-7541, 1998.
8. J.M. Chandonia and M. Karplus, "Neural networks for secondary structure and structural class predictions", Protein Science, vol. 4, pp. 275-285, 1995.
9. T.R.J. Cheng, Y.E. Yin and S. Erickson-Viitanen, "Mutagenesis of protease cleavage sites in the human immunodeficiency virus type 1 gag polyprotein", Journal of Virology, vol. 65, pp. 922-930, 1991.
10. K.C. Chou, "Prediction of Human Immunodeficiency Virus protease cleavage sites in proteins", Analytical Biochemistry, vol. 233, pp. 1-14, 1996.
11. J.S. Cottrell, "Protein identification by peptide mass finger-printing", Peptide Research, vol. 7, pp. 115, 1994.
12. G.B. Dreyer, D.M. Lambert, T.D. Meek, T.J. Carr, T.A. Tomaszek, A.V. Fernandez, H. Bartus and E. Cacciavillani, "Hydroxyethylene isostere inhibitors of human immunodeficiency virus-1 protease: structure-activity analysis using enzyme kinetics, X-ray crystallography, and infected T-cell assays", Biochemistry, vol. 31, pp. 6646-6659, 1992.
13. E.A. Ferran and P. Ferrara, "Topological maps of protein sequences", Biological Cybernetics, vol. 65, pp. 451-458, 1991.
14. S. Fournout, F. Roquet, S.L. Salhi, R. Seyer, V. Valverde, J.M. Masson, P. Jouin, B. Pau, M. Nicolas and V. Hanin, "Development and standardization of an immuno-quantified solid phase assay for HIV-1 aspartyl protease activity and its application to the evaluation of inhibitor", Analytical Chemistry, vol. 69, pp. 1746-1752, 1997.
15. M.P. Glenn, L.K. Pattenden, R.C. Reid, D.P. Tyssen, J.D.A. Tyndall, C.J. Birch and D.P. Fairlie, "Beta-strand mimicking macrocyclic amino acids: templates for protease inhibitors with antiviral activity", Journal of Medicinal Chemistry, vol. 45, pp. 371-381, 2002.
16. C.U.T. Hellen, H.G. Krausslich and E. Wimmer, "Proteolytic processing of polyproteins in the replication of RNA viruses", Biochemistry, vol. 28, pp. 9881-9890, 1989.
17. L. Hong, "Active-site mobility in human immunodeficiency virus, type 1, protease as demonstrated by crystal structure of A28s mutant", Protein Science, vol. 7, pp. 300-305, 1998.
18. M.S. Johnson and J.P. Overington, "A structural basis for sequence comparisons-an evaluation of scoring methodologies", J. Mol. Biol., vol. 233, pp. 716-738, 1993.
19. D.B. Kassel, M.D. Green, R.S. Wehbie, R. Swanstrom and J. Berman, "HIV-1 protease specificity derived from a complex mixture of synthetic substrates", Analytical Biochemistry, vol. 228, pp. 259-266, 1995.
20. S. Kawabata, T. Miura, T. Morita, H. Kato, K. Fujikawa, I. Sadaaki, K. Takada, T. Kimura and S. Sakakibara, "Highly sensitive peptide-4-methylcoumaryl-7-amide substrates for blood-clotting proteases and trypsin", Eur J Biochem, vol. 172, pp. 17-25, 1988.
21. B. Keil, Specificity of proteolysis, Springer-Verlag Berlin-Heidelberg-NewYork, 1992.
22. A. Lesner, K. Brzozowski, G. Kupryszewski and K. Rolka, "Design, chemical synthesis and kinetic studies of trypsin chromogenic substrates based on the proteinase binding loop of Cucurbita maxima trypsin inhibitor (CMTI-III)", Biochem Biophys Res Comms, vol. 269, pp. 81-84, 2000.
23. M. Marastoni, F. Bortolotti, S. Salvadori and R. Tomatis, "Structure-activity relationships of HIV-1 protease inhibitors containing gem-diaminoserine core unit", Arzneimittel-Forschung, vol. 48, pp. 709-712, 1998.
24. B.J. McRae, K. Kurachi, R.L. Helmark, K. Fujikawa, E.W. Davie and J.C. Powers, "Mapping the active sites of bovine thrombin, Factor IXa, Factor Xa, Factor XIa, Factor XIIa, plasma kallikrein and trypsin with amino acid and peptide thioesters: development of new sensitive substrates", Biochemistry, vol. 20, pp.7196-7206, 1981.
25. J. Moody and C. Darken, "Learning with localized receiptive fields", in T. Sejnowski, D. Touretzky, and G. Hinton (eds) Connectionist Models Summer School, Carnegie Mellon University, 1988.
26. A. Narayanan, X.K. Wu and Z.R. Yang, "Mining viral protease data to extract cleavage knowledge", Bioinformatics, (in press).
27. N. Okimoto, "Protein hydrolysis mechanism of HIV-1 protease investigation by the ab initio MO calculations", RIKEN Review, vol. 29, pp. 100-102, 2000.
28. http://www.expasy.org/tools/peptidecutter/peptidecutterenzymes.html
29. A.D. Pivazyan, D.S. Matteson, L. Fabry-Asztalos, R.P. Singh, P.F. Lin, W. Blair, K. Guo, B. Robinson and W.H. Prusoff, "Inhibition of HIV-1 protease by a boron-modified polypeptide", Biochemical Pharmacology, vol. 60, pp. 927-936, 2000.
30. L. Polgar, Z. Szeltner and I. Boros, "Substrate-dependent mechanisms in the catalysis of human immunodeficiency virus protease", Biochemistry, vol. 33, pp. 9351-9357, 1994.
31. G. Pollastri, D. Przybylski, B Rost and P. Baldi, "Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles", Proteins, vol. 47, pp. 228-235, 2002.
32. R.A. Poorman, A.G. Tomasselli, R.L. Heinrikson and F.J. Kezdy, "A cumulative specificity model for protease from human immunodeficiency virus types 1 and 2, inferred from statistical analysis of an extended substrate data base", The Journal of Biological Chemistry, vol. 22, pp. 14554-14561, 1991.
33. M. Pozsgay, G.C.S. Szbabo, S. Bajusz, R. Simonsson, R. Gaspar and P. Elodi, "Investigation of the substrate-binding site of trypsin by the aid of tripeptidyl-p-nitroanilide substrates", Eur J Biochem/FEBS, vol. 115, pp.497-502, 1981.
34. M. Reczko, "Protein secondary structure prediction with partially recurrent neural networks", SAR and QSAR in Environmental Research, vol. 1, pp. 153-159, 1993.
35. S.H. Reich, M. Melnick, M.J. Pino, M.A. Fuhry, A.J. Trippe, K. Appelt, J.F. Davies, B.W. Wu and L. Musick, "Structure-based design and synthesis of substituted 2-butanols as non-peptidic inhibitors of HIV protease: secondary amide series", Journal of Medicinal Chemistry, vol. 39, pp. 2781-2794, 1996.
36. C.D. Rosin, R.K. Belew, G.M. Morris, A.J. Olson and D.S. Goodsell, "Coevolutionary analysis of resistance-evading peptidominetic inhibitors of HIV-1 protease", Proc. Natl. Acad. Sci. USA, vol. 96, pp. 1369-1374, 1999.
37. I. Schechter and A. Berger, "On the size of the active site in proteases. I. Papain", Biochem Biophys Res Comm, vol 27, pp.157, 1967.
38. T.B. Thompson, K.C. Chou and C.T. Zheng, "Neural network prediction of the HIV-1 protease cleavage sites", J. Theor. Biol. vol. 177, pp. 369-379, 1995.
39. H. Toh, M. Ono, K. Saigo and T. Miyata, "Retroviral protease-like sequence in the yeast transposon Ty1", Nature, 315, pp. 691-692, 1985.
40. A. Tossi, N. Antcheva, D. Romeo and S. Miertus, "Development of pseudopeptide inhibitors of HIV-1 aspartic protease: analysis and tuning of the subsite specificity", Peptide Research, vol. 8, pp. 328-334, 1995.
41. T.T. Tran, N. Patinoa, R. Condoma, T. Frogiera and R. Guedja, "Fluorinated peptides incorporating a 4-fluoroproline residue as potential inhibitors of HIV protease", Journal of Fluorine Chemistry, vol. 82, pp. 125-130, 1997.
42. A. Wittinghofer, R. Frank and R. Leberman, "Composition and properties of trypsin-cleaved elongation factor Tu", Eur J Biochem, vol 108, pp. 423-431, 1980
43. C. Wu, G. Whitson, J. McLarty, A. Ermongkonchai and T.C. Chang, "Protein classification artificial neural system", Protein Science, vol. 1, pp. 667-677, 1992.