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Volumn 19, Issue 4, 2006, Pages 401-407

A bio-basis function neural network for protein peptide cleavage activity characterisation

Author keywords

Bio basis functions; Mutation matrix; Neural learning; Protease cleavage site prediction and characterisation

Indexed keywords

AMINO ACIDS; CLASSIFIERS; LEARNING ALGORITHMS; PROTEINS; RADIAL BASIS FUNCTION NETWORKS;

EID: 33745043489     PISSN: 08936080     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.neunet.2005.07.015     Document Type: Article
Times cited : (10)

References (44)
  • 1
    • 0000874557 scopus 로고
    • Theoretical foundations of the potential function method in pattern recognition learning
    • Aizerman M.A., Braverman E.M., and Rozonoer L.I. Theoretical foundations of the potential function method in pattern recognition learning. Automation and Remote Control 25 (1964) 821-837
    • (1964) Automation and Remote Control , vol.25 , pp. 821-837
    • Aizerman, M.A.1    Braverman, E.M.2    Rozonoer, L.I.3
  • 2
    • 0025814729 scopus 로고
    • Identification of a new motif on nucleic acid sequence data using Kohonen's self-organising map
    • Arrigo P., Giuliano F., Scalia F., Rapallo A., and Damiani G. Identification of a new motif on nucleic acid sequence data using Kohonen's self-organising map. CABIOS 7 (1991) 353-357
    • (1991) CABIOS , vol.7 , pp. 353-357
    • Arrigo, P.1    Giuliano, F.2    Scalia, F.3    Rapallo, A.4    Damiani, G.5
  • 4
    • 0043092351 scopus 로고    scopus 로고
    • Geno2pheno: Estimating phenotypic drug resistance from HIV-1 genotypes
    • Beerenwinkel N., Daumer M., Oette M., Korn K., Hoffmann D., Kaiser R., et al. Geno2pheno: Estimating phenotypic drug resistance from HIV-1 genotypes. NAR 31 (2003) 3850-3855
    • (2003) NAR , vol.31 , pp. 3850-3855
    • Beerenwinkel, N.1    Daumer, M.2    Oette, M.3    Korn, K.4    Hoffmann, D.5    Kaiser, R.6
  • 5
    • 0037062513 scopus 로고    scopus 로고
    • Diversity and complexity of HIV-1 drug resistance: A bioinformatics approach to predicting phenotype from genotype
    • Beerenwinkel N., Schmidt B., Walter H., Kaiser R., Lengauer T., Hoffmann D., et al. Diversity and complexity of HIV-1 drug resistance: A bioinformatics approach to predicting phenotype from genotype. PNAS 99 (2002) 8271-8276
    • (2002) PNAS , vol.99 , pp. 8271-8276
    • Beerenwinkel, N.1    Schmidt, B.2    Walter, H.3    Kaiser, R.4    Lengauer, T.5    Hoffmann, D.6
  • 6
    • 0025134507 scopus 로고
    • Efficient recognition of immunoglobulin domains from amino acid sequences using a neural network
    • Bengio Y., and Pouliot Y. Efficient recognition of immunoglobulin domains from amino acid sequences using a neural network. CABIOS 6 (1990) 319-324
    • (1990) CABIOS , vol.6 , pp. 319-324
    • Bengio, Y.1    Pouliot, Y.2
  • 7
    • 0842301301 scopus 로고    scopus 로고
    • Reduced bio-basis function neural networks in prediction of phosphorylation sites, a comparative study
    • Berry E., Dalby A., and Yang Z.R. Reduced bio-basis function neural networks in prediction of phosphorylation sites, a comparative study. Computational Biology and Chemistry 28 (2004) 75-85
    • (2004) Computational Biology and Chemistry , vol.28 , pp. 75-85
    • Berry, E.1    Dalby, A.2    Yang, Z.R.3
  • 9
    • 0033579464 scopus 로고    scopus 로고
    • Sequence and structure based prediction of eukaryotic protein phosphorylation sites
    • Blom N., Gammeltoft S., and Brunak S. Sequence and structure based prediction of eukaryotic protein phosphorylation sites. Journal of Molecular biology 294 (1999) 1351-1362
    • (1999) Journal of Molecular biology , vol.294 , pp. 1351-1362
    • Blom, N.1    Gammeltoft, S.2    Brunak, S.3
  • 10
    • 0032017815 scopus 로고    scopus 로고
    • Artificial neural network model for predicting HIV protease cleavage sites in protein
    • Cai Y.D., and Chou K.C. Artificial neural network model for predicting HIV protease cleavage sites in protein. Advances in Engineering Software 29 (1998) 119-128
    • (1998) Advances in Engineering Software , vol.29 , pp. 119-128
    • Cai, Y.D.1    Chou, K.C.2
  • 11
    • 0029343956 scopus 로고
    • Fast orthogonal least squares algorithm for efficient subset model selection
    • Chen S., and Wigger J. Fast orthogonal least squares algorithm for efficient subset model selection. IEEE Transactions on Signal Processing 43 (1995) 1713-1714
    • (1995) IEEE Transactions on Signal Processing , vol.43 , pp. 1713-1714
    • Chen, S.1    Wigger, J.2
  • 12
    • 0029341753 scopus 로고
    • Approximation capability to functions of several variables, nonlinear functionals, and operators by radial basis function neural networks
    • Chen T., and Chen H. Approximation capability to functions of several variables, nonlinear functionals, and operators by radial basis function neural networks. IEEE Transactions on Neural Networks 6 (1995) 904-910
    • (1995) IEEE Transactions on Neural Networks , vol.6 , pp. 904-910
    • Chen, T.1    Chen, H.2
  • 13
    • 0029733768 scopus 로고    scopus 로고
    • Gradient radial basis function networks for nonlinear and nonstationary time series prediction
    • Chng E.S., Chen S., and Mulgrew B. Gradient radial basis function networks for nonlinear and nonstationary time series prediction. IEEE Transactions on Neural Networks 7 (1996) 190-194
    • (1996) IEEE Transactions on Neural Networks , vol.7 , pp. 190-194
    • Chng, E.S.1    Chen, S.2    Mulgrew, B.3
  • 14
    • 0028429419 scopus 로고
    • Protein identification by peptide mass fingerprinting
    • Cottrell J.S. Protein identification by peptide mass fingerprinting. Peptide Research 7 (1994) 115
    • (1994) Peptide Research , vol.7 , pp. 115
    • Cottrell, J.S.1
  • 16
    • 0000228203 scopus 로고
    • A model of evolutionary change in proteins. Matrices for detecting distant relationships
    • Dayhoff M.O. (Ed), National Biomedical Research Foundation, Washington, DC
    • Dayhoff M.O., Schwartz R.M., and Orcutt B.C. A model of evolutionary change in proteins. Matrices for detecting distant relationships. In: Dayhoff M.O. (Ed). Atlas of protein sequence and structure Vol. 5 (1978), National Biomedical Research Foundation, Washington, DC 345-358
    • (1978) Atlas of protein sequence and structure , vol.5 , pp. 345-358
    • Dayhoff, M.O.1    Schwartz, R.M.2    Orcutt, B.C.3
  • 17
    • 0037248697 scopus 로고    scopus 로고
    • Predicting HIV drug resistance with neural networks
    • Draghici S., and Potter R.B. Predicting HIV drug resistance with neural networks. Bioinformatics 19 (2003) 98-107
    • (2003) Bioinformatics , vol.19 , pp. 98-107
    • Draghici, S.1    Potter, R.B.2
  • 18
    • 0031912107 scopus 로고    scopus 로고
    • Prediction of protein hydration sites from sequence by modular neural networks
    • Ehrlich L., Reczko M., Bohr H., and Wade R.C. Prediction of protein hydration sites from sequence by modular neural networks. Protein Engineering 11 (1998) 11-19
    • (1998) Protein Engineering , vol.11 , pp. 11-19
    • Ehrlich, L.1    Reczko, M.2    Bohr, H.3    Wade, R.C.4
  • 19
    • 0026268095 scopus 로고
    • Topological maps of protein sequences
    • Ferran E.A., and Ferrara P. Topological maps of protein sequences. Biological Cybernetics 65 (1991) 451-458
    • (1991) Biological Cybernetics , vol.65 , pp. 451-458
    • Ferran, E.A.1    Ferrara, P.2
  • 20
    • 0027764341 scopus 로고
    • A hybrid method to cluster protein sequences based on statistics and artificial neural networks
    • Ferran E.A., and Pflugfelder B. A hybrid method to cluster protein sequences based on statistics and artificial neural networks. CABIOS 9 (1993) 671-680
    • (1993) CABIOS , vol.9 , pp. 671-680
    • Ferran, E.A.1    Pflugfelder, B.2
  • 21
    • 0027147482 scopus 로고
    • Improvement of downstream processing of recombinant proteins by means of genetic engineering methods
    • Flaschel E., and Friehs K. Improvement of downstream processing of recombinant proteins by means of genetic engineering methods. Biotechnology Advances 11 (1993) 31-78
    • (1993) Biotechnology Advances , vol.11 , pp. 31-78
    • Flaschel, E.1    Friehs, K.2
  • 22
    • 0042674397 scopus 로고    scopus 로고
    • Using a neural network and spatial clustering to predict the location of active sites in enzymes
    • Gutteridge A., Bartlett G.J., and Thornton J.M. Using a neural network and spatial clustering to predict the location of active sites in enzymes. Journal of Molecular Biology 330 (2003) 719-734
    • (2003) Journal of Molecular Biology , vol.330 , pp. 719-734
    • Gutteridge, A.1    Bartlett, G.J.2    Thornton, J.M.3
  • 25
    • 0002714543 scopus 로고    scopus 로고
    • Making large-scale SVM learning practical
    • Scholkopf B., and Burges C. (Eds), MIT Press, Cambridge, MA
    • Joachims T. Making large-scale SVM learning practical. In: Scholkopf B., and Burges C. (Eds). Advances in kernel methods-support vector learning (1999), MIT Press, Cambridge, MA
    • (1999) Advances in kernel methods-support vector learning
    • Joachims, T.1
  • 26
    • 0027361123 scopus 로고
    • A structural basis for sequence comparisons-An evaluation of scoring methodologies
    • Johnson M.S., and Overington J.P. A structural basis for sequence comparisons-An evaluation of scoring methodologies. Journal of Molecular Biology 233 (1993) 716-738
    • (1993) Journal of Molecular Biology , vol.233 , pp. 716-738
    • Johnson, M.S.1    Overington, J.P.2
  • 27
    • 0026135904 scopus 로고
    • Radial basis function networks for classifying process faults
    • Leonard J.A., and Kramer M.A. Radial basis function networks for classifying process faults. IEEE Control Systems April (1991) 31-38
    • (1991) IEEE Control Systems , vol.April , pp. 31-38
    • Leonard, J.A.1    Kramer, M.A.2
  • 28
    • 0016772212 scopus 로고
    • Comparison of the predicted and observed secondary structure of T4 phage lysozyme
    • Matthews B.W. Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochimica et Biophysica Acta 405 (1975) 442-451
    • (1975) Biochimica et Biophysica Acta , vol.405 , pp. 442-451
    • Matthews, B.W.1
  • 29
    • 0019814899 scopus 로고
    • 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
    • McRae B.J., Kurachi K., Helmark R.L., Fujikawa K., Davie E.W., and Powers J.C. 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 20 (1981) 7196-7206
    • (1981) Biochemistry , vol.20 , pp. 7196-7206
    • McRae, B.J.1    Kurachi, K.2    Helmark, R.L.3    Fujikawa, K.4    Davie, E.W.5    Powers, J.C.6
  • 30
    • 0018079655 scopus 로고
    • Basic principles of ROC analysis
    • Metz C.E. Basic principles of ROC analysis. Seminars in Nuclear Medicine 8 (1978) 283-298
    • (1978) Seminars in Nuclear Medicine , vol.8 , pp. 283-298
    • Metz, C.E.1
  • 31
    • 0002773313 scopus 로고
    • Learning with localized receiptive fields
    • Sejnowski T., Touretzky D., and Hinton G. (Eds), Carnegie Mellon University, Pittsburgh, PA
    • Moody J., and Darken C. Learning with localized receiptive fields. In: Sejnowski T., Touretzky D., and Hinton G. (Eds). Connectionist models summer school (1988), Carnegie Mellon University, Pittsburgh, PA
    • (1988) Connectionist models summer school
    • Moody, J.1    Darken, C.2
  • 32
    • 0000672424 scopus 로고
    • Fast learning in networks of locally tuned units
    • Moody J., and Darken C. Fast learning in networks of locally tuned units. Neural Computation 1 (1989) 281-294
    • (1989) Neural Computation , vol.1 , pp. 281-294
    • Moody, J.1    Darken, C.2
  • 33
    • 0030110770 scopus 로고    scopus 로고
    • Upstream strategies to minimize proteolytic degradation upon recombinant production in Escherichia coli
    • Murby M., Uhlen M., and Stahl S. Upstream strategies to minimize proteolytic degradation upon recombinant production in Escherichia coli. Protein Expression and Purification 7 (1996) 129-136
    • (1996) Protein Expression and Purification , vol.7 , pp. 129-136
    • Murby, M.1    Uhlen, M.2    Stahl, S.3
  • 34
    • 0141721892 scopus 로고    scopus 로고
    • Mining viral protease data to extract cleavage knowledge
    • Narayanan A., Wu X.K., and Yang Z.R. Mining viral protease data to extract cleavage knowledge. Bioinformatics 18 (2002) 5-13
    • (2002) Bioinformatics , vol.18 , pp. 5-13
    • Narayanan, A.1    Wu, X.K.2    Yang, Z.R.3
  • 35
    • 0030614959 scopus 로고    scopus 로고
    • Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites
    • Nielsen H., Engelbrecht J., Brunak S., and von Heijne G. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Engineering 10 (1997) 1-6
    • (1997) Protein Engineering , vol.10 , pp. 1-6
    • Nielsen, H.1    Engelbrecht, J.2    Brunak, S.3    von Heijne, G.4
  • 36
    • 0025490985 scopus 로고
    • Networks for approximation and learning
    • Poggio T., and Girosi F. Networks for approximation and learning. Proceedings of the IEEE 78 (1990) 1481-1497
    • (1990) Proceedings of the IEEE , vol.78 , pp. 1481-1497
    • Poggio, T.1    Girosi, F.2
  • 37
    • 0023803244 scopus 로고
    • Predicting the secondary structure of globular proteins using neural network models
    • Qian N., and Sejnowski T.J. Predicting the secondary structure of globular proteins using neural network models. Journal of Molecular Biology 202 (1988) 865-884
    • (1988) Journal of Molecular Biology , vol.202 , pp. 865-884
    • Qian, N.1    Sejnowski, T.J.2
  • 39
    • 0033027794 scopus 로고    scopus 로고
    • Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation
    • Tamayo P., Slonim D., Mesirov J., Zhu Q., Kitareewan S., Dmitrovsky E., et al. Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation. PNAS 96 (1999) 2907-2912
    • (1999) PNAS , vol.96 , pp. 2907-2912
    • Tamayo, P.1    Slonim, D.2    Mesirov, J.3    Zhu, Q.4    Kitareewan, S.5    Dmitrovsky, E.6
  • 40
    • 0029595415 scopus 로고
    • Neural network prediction of the HIV-1 protease cleavage sitesy
    • Thompson T.B., Chou K.C., and Zheng C. Neural network prediction of the HIV-1 protease cleavage sitesy. Journal of Theoretical Biology 177 (1995) 369-379
    • (1995) Journal of Theoretical Biology , vol.177 , pp. 369-379
    • Thompson, T.B.1    Chou, K.C.2    Zheng, C.3
  • 43
    • 0031595301 scopus 로고    scopus 로고
    • Self-organising tree growing network for classifying amino acids
    • Wang H.C., Dopazo J., and Carazo J.M. Self-organising tree growing network for classifying amino acids. Bioinformatics 14 (1998) 376-377
    • (1998) Bioinformatics , vol.14 , pp. 376-377
    • Wang, H.C.1    Dopazo, J.2    Carazo, J.M.3


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