메뉴 건너뛰기




Volumn 35, Issue 1, 2005, Pages 100-106

Orthogonal kernel machine for the prediction of functional sites in proteins

Author keywords

Bioinformatics; Kernel based approach and orthogonal method; Pattern recognition

Indexed keywords

ALGORITHMS; AMINO ACIDS; FUNCTIONS; MATRIX ALGEBRA; NEURAL NETWORKS; PROTEINS;

EID: 13644251956     PISSN: 10834419     EISSN: None     Source Type: Journal    
DOI: 10.1109/TSMCB.2004.840723     Document Type: Article
Times cited : (16)

References (43)
  • 2
    • 0028289467 scopus 로고
    • "Issues in searching molecular sequence databases"
    • S. F. Altschul, M. S. Boguski, W. Gish, and J. C. Wootton, "Issues in searching molecular sequence databases," Nature Genet., vol. 6, pp. 119-129, 1994.
    • (1994) Nature Genet. , vol.6 , pp. 119-129
    • Altschul, S.F.1    Boguski, M.S.2    Gish, W.3    Wootton, J.C.4
  • 4
    • 0028468293 scopus 로고
    • "Using mutual information for selecting features in supervised neural net learning"
    • Jul
    • R. Battiti, "Using mutual information for selecting features in supervised neural net learning," IEEE Trans. Neural Netw.. vol. 5, no. 4, pp. 537-550, Jul. 1994.
    • (1994) IEEE Trans. Neural Netw. , vol.5 , Issue.4 , pp. 537-550
    • Battiti, R.1
  • 5
    • 0025134507 scopus 로고
    • "Efficient recognition of immunological domains from amino acid sequences using a neural network"
    • Y. Bengio and Y. Pouliot, "Efficient recognition of immunological domains from amino acid sequences using a neural network," CABIOS, vol. 6, pp. 319-324, 1990.
    • (1990) CABIOS , vol.6 , pp. 319-324
    • Bengio, Y.1    Pouliot, Y.2
  • 6
    • 0842301301 scopus 로고    scopus 로고
    • "Reduced bio-basis function neural networks in prediction of phosphorylation sites, a comparative study"
    • E. Berry, A. Dalby, and Z. R. Yang, "Reduced bio-basis function neural networks in prediction of phosphorylation sites, a comparative study," Comput. Biol. Chem., vol. 28, pp. 75-85, 2004.
    • (2004) Comput. Biol. Chem. , vol.28 , pp. 75-85
    • Berry, E.1    Dalby, A.2    Yang, Z.R.3
  • 7
    • 0033579464 scopus 로고    scopus 로고
    • "Sequence and structure based prediction of eukaryotic protein phosphorylation sites"
    • N. Blom, S. Gammeltoft, and S. Brunak, "Sequence and structure based prediction of eukaryotic protein phosphorylation sites," J. Mol. Biol., vol. 294, pp. 1351-1362. 1999.
    • (1999) J. Mol. Biol. , vol.294 , pp. 1351-1362
    • Blom, N.1    Gammeltoft, S.2    Brunak, S.3
  • 8
    • 0035023445 scopus 로고    scopus 로고
    • "Predicting protein-protein interactions from primary structure"
    • J. R. Bock and D. A. Gough, "Predicting protein-protein interactions from primary structure," Bioinform., vol. 17, pp. 455-460, 2001.
    • (2001) Bioinform. , vol.17 , pp. 455-460
    • Bock, J.R.1    Gough, D.A.2
  • 9
    • 0030589677 scopus 로고    scopus 로고
    • "Artificial neural network model for predicting the specificity of GalNAc-transferase"
    • Y. D. Cai and K. C. Chou, "Artificial neural network model for predicting the specificity of GalNAc-transferase," Anal. Biochem. vol. 243, pp. 284-285, 1996.
    • (1996) Anal. Biochem. , vol.243 , pp. 284-285
    • Cai, Y.D.1    Chou, K.C.2
  • 10
    • 0032017815 scopus 로고    scopus 로고
    • "Artificial neural network model for predicting HIV protease cleavage sites in protein"
    • Y. D. Cai and K. C. Chou, "Artificial neural network model for predicting HIV protease cleavage sites in protein," Adv. Eng. Softw. vol. 29, pp. 119-128, 1998.
    • (1998) Adv. Eng. Softw. , vol.29 , pp. 119-128
    • Cai, Y.D.1    Chou, K.C.2
  • 11
    • 0036154920 scopus 로고    scopus 로고
    • "Support vector machines for predicting the specificity of GalNAc-transferase"
    • Y. D. Cai, X. J. Liu, X. B. Xu, and K. C. Chou, "Support vector machines for predicting the specificity of GalNAc-transferase," Peptides, vol. 23, pp. 205-208, 2002.
    • (2002) Peptides , vol.23 , pp. 205-208
    • Cai, Y.D.1    Liu, X.J.2    Xu, X.B.3    Chou, K.C.4
  • 12
    • 0026116468 scopus 로고
    • "Orthogonal least squares learning algoritm for radial basis function networks"
    • Mar
    • S. Chen, C. F. N. Cowan, and P. M. Grant, "Orthogonal least squares learning algoritm for radial basis function networks," IEEE Trans. Neural Netw., vol. 2, no. 2, pp. 302-309, Mar. 1991.
    • (1991) IEEE Trans. Neural Netw. , vol.2 , Issue.2 , pp. 302-309
    • Chen, S.1    Cowan, C.F.N.2    Grant, P.M.3
  • 13
    • 0035030201 scopus 로고    scopus 로고
    • "Using subsite coupling to predict signal peptides"
    • K. C. Chou, "Using subsite coupling to predict signal peptides," Protein Eng., vol. 14, pp. 75-79, 2001.
    • (2001) Protein Eng. , vol.14 , pp. 75-79
    • Chou, K.C.1
  • 14
    • 0000228203 scopus 로고
    • "A model of evolutionary change in proteins"
    • M. O. Dayhoff, Ed. Washington, DC: Nat.l Biomed. Res. Foundation, Atlas of Protein Sequence and Structure
    • M. O. Dayhoff, R. M. Schwartz, and B. C. Orcutt, "A model of evolutionary change in proteins," in Matrices for Detecting Distant Relationships, M. O. Dayhoff, Ed. Washington, DC: Nat.l Biomed. Res. Foundation, 1978, vol. 5, Atlas of Protein Sequence and Structure, pp. 345-358.
    • (1978) Matrices for Detecting Distant Relationships , vol.5 , pp. 345-358
    • Dayhoff, M.O.1    Schwartz, R.M.2    Orcutt, B.C.3
  • 17
    • 0036122073 scopus 로고    scopus 로고
    • "Prediction of protein-protein interaction sites in heterocomplexes with neural networks"
    • P. Fariselli, F. Pazos, A. Valencia, and R. Casadio, "Prediction of protein-protein interaction sites in heterocomplexes with neural networks," Eur. J. Biochem., vol. 269, pp. 1356-1361, 2002.
    • (2002) Eur. J. Biochem. , vol.269 , pp. 1356-1361
    • Fariselli, P.1    Pazos, F.2    Valencia, A.3    Casadio, R.4
  • 18
    • 0024963567 scopus 로고
    • "Signal sequences"
    • L. M. Gierasch, "Signal sequences," Biochem., vol. 28, pp. 923-930, 1989.
    • (1989) Biochem. , vol.28 , pp. 923-930
    • Gierasch, L.M.1
  • 19
    • 0042674397 scopus 로고    scopus 로고
    • "Using a neural network and spatial clustering to predict the location of active sites in enzymes"
    • A. Gutteridge, G. J. Bartlett, and J. M. Thornton, "Using a neural network and spatial clustering to predict the location of active sites in enzymes," J. Molec. Biol., vol. 330, pp. 719-734, 2003.
    • (2003) J. Molec. Biol. , vol.330 , pp. 719-734
    • Gutteridge, A.1    Bartlett, G.J.2    Thornton, J.M.3
  • 20
    • 0026458378 scopus 로고
    • "Amino acid substitution matrices from protein blocks"
    • S. Henikoff and J. G. Henikoff, "Amino acid substitution matrices from protein blocks," in Proc. Natl. Academy Science, vol. 89, 1992, pp. 10915-10919.
    • (1992) Proc. Natl. Academy Science , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 21
    • 0027317580 scopus 로고
    • "Performance evaluation of amino acid substitution matrices"
    • S. Henikoff and J. G. Henikoff, "Performance evaluation of amino acid substitution matrices," Proteins: Struct., Funct. Genet., vol. 17, pp. 49-61, 1993.
    • (1993) Proteins: Struct., Funct. Genet. , vol.17 , pp. 49-61
    • Henikoff, S.1    Henikoff, J.G.2
  • 22
    • 0002714543 scopus 로고    scopus 로고
    • "Making large-scale SVM learning practical"
    • B. Scholkopf and C. Burges, Eds. Cambridge, MA: MIT Press
    • T. Joachims, "Making large-scale SVM learning practical," in Advances in Kernel Methods - Support Vector Learning, B. Scholkopf and C. Burges, Eds. Cambridge, MA: MIT Press, 1999.
    • (1999) Advances in Kernel Methods - Support Vector Learning
    • Joachims, T.1
  • 23
    • 0027361123 scopus 로고
    • "A structural basis for sequence comparisons - An evaluation of scoring methodologies"
    • M. S. Johnson and J. P. Overington, "A structural basis for sequence comparisons - an evaluation of scoring methodologies," J. Molec. Biol., vol. 233, pp. 716-738, 1993.
    • (1993) J. Molec. Biol. , vol.233 , pp. 716-738
    • Johnson, M.S.1    Overington, J.P.2
  • 24
    • 0031565729 scopus 로고    scopus 로고
    • "Analysis of protein-protein interaction sites using surface parches"
    • S. Jones and J. M. Thornton, "Analysis of protein-protein interaction sites using surface parches," J. Molec. Biol., vol. 272, pp. 121-132, 1997.
    • (1997) J. Molec. Biol. , vol.272 , pp. 121-132
    • Jones, S.1    Thornton, J.M.2
  • 25
    • 0018079655 scopus 로고
    • "Basic principles of ROC analysis"
    • C. E. Metz, "Basic principles of ROC analysis," Seminars Nuclear Medicine, vol. 8, pp. 283-298, 1978.
    • (1978) Seminars Nuclear Medicine , vol.8 , pp. 283-298
    • Metz, C.E.1
  • 26
    • 1642333377 scopus 로고    scopus 로고
    • "Prediction of protein-protein interaction sites using support vector machines"
    • Y. Minakuchi, K. Satou, and A. Konagaya, "Prediction of protein-protein interaction sites using support vector machines," Genome Informatics vol. 13, pp. 322-323, 2002.
    • (2002) Genome Informatics , vol.13 , pp. 322-323
    • Minakuchi, Y.1    Satou, K.2    Konagaya, A.3
  • 27
    • 0017535866 scopus 로고
    • "A branch and bound algorithm for feature subset selection"
    • Aug
    • P. M. Narendra and K. Fukunaga, "A branch and bound algorithm for feature subset selection," IEEE Trans. Comput., vol. 26, no. 8, pp. 917-922, Aug. 1977.
    • (1977) IEEE Trans. Comput. , vol.26 , Issue.8 , pp. 917-922
    • Narendra, P.M.1    Fukunaga, K.2
  • 28
    • 0141721892 scopus 로고    scopus 로고
    • "Mining vital protease data to extract cleavage knowledge"
    • A. Narayanan, X. K. Wu, and Z. R. Yang, "Mining vital protease data to extract cleavage knowledge," Bioinformat., vol. 18, pp. 5-13, 2002.
    • (2002) Bioinformat. , vol.18 , pp. 5-13
    • Narayanan, A.1    Wu, X.K.2    Yang, Z.R.3
  • 29
    • 0030614959 scopus 로고    scopus 로고
    • "Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites"
    • H. Nielsen, J. Engelbrecht, S. Brunak, and G. von Heijne, "Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites," Protein Engi., vol. 10, pp. 1-6, 1997.
    • (1997) Protein Engi. , vol.10 , pp. 1-6
    • Nielsen, H.1    Engelbrecht, J.2    Brunak, S.3    Heijne, G.4
  • 30
    • 0026345896 scopus 로고
    • "A cumulative specificity model for protease from human immunodeficiency virus types 1 and 2, inferred from statistical analysis of an extended substrate data base"
    • 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," J. Biol. Chem., vol. 22, pp. 14554-14561, 1991.
    • (1991) J. Biol. Chem. , vol.22 , pp. 14554-14561
    • Poorman, R.A.1    Tomasselli, A.G.2    Heinrikson, R.L.3    Kezdy, F.J.4
  • 31
    • 0023803244 scopus 로고
    • "Predicting the secondary structure of globular proteins using neural network models"
    • N. Qian and T. J. Sejnowski "Predicting the secondary structure of globular proteins using neural network models," J. Molec. Biol., vol. 202, pp. 865-884, 1988.
    • (1988) J. Molec. Biol. , vol.202 , pp. 865-884
    • Qian, N.1    Sejnowski, T.J.2
  • 32
    • 0026471714 scopus 로고
    • "Transport of proteins across the endoplasmic reticulum membrane"
    • T. A. Rapoport, "Transport of proteins across the endoplasmic reticulum membrane," Science, vol. 258, pp. 931-936, 1992.
    • (1992) Science , vol.258 , pp. 931-936
    • Rapoport, T.A.1
  • 33
    • 0029595415 scopus 로고
    • "Neural network prediction of the HIV-1 protease cleavage sitesy"
    • T. B. Thompson, K. C. Chou, and C. Zheng, "Neural network prediction of the HIV-1 protease cleavage sitesy," J. Theoret. Biol., vol. 177, pp. 369-379, 1995.
    • (1995) J. Theoret. Biol. , vol.177 , pp. 369-379
    • Thompson, T.B.1    Chou, K.C.2    Zheng, C.3
  • 34
    • 0141506120 scopus 로고    scopus 로고
    • "Characterizing proteolytic cleavage site activity using bio-basis function neural networks"
    • R. Thomson, C. Hodgman, Z. R. Yang, and A. Doyle, "Characterizing proteolytic cleavage site activity using bio-basis function neural networks," Bioinform., vol. 19, pp. 1741-1747, 2003.
    • (2003) Bioinform. , vol.19 , pp. 1741-1747
    • Thomson, R.1    Hodgman, C.2    Yang, Z.R.3    Doyle, A.4
  • 37
    • 0025297583 scopus 로고
    • "The signal peptide"
    • G. von Heijne, "The signal peptide," J. Membrane Biol., vol. 115, pp. 195-201, 1990.
    • (1990) J. Membrane Biol. , vol.115 , pp. 195-201
    • Heijne, G.1
  • 39
    • 0033908160 scopus 로고    scopus 로고
    • "Applying a robust heteroscedastic neural network to analog fault detection and classification"
    • Z. R. Yang and M. Zwolinski, "Applying a robust heteroscedastic neural network to analog fault detection and classification," IEEE Trans. Computer-Aided Design Integr. Circuits Syst., vol. 19, no. 1, pp. 129-141, 2000.
    • (2000) IEEE Trans. Computer-Aided Design Integr. Circuits Syst. , vol.19 , Issue.1 , pp. 129-141
    • Yang, Z.R.1    Zwolinski, M.2
  • 40
    • 1842439981 scopus 로고    scopus 로고
    • "Predicting the O-linkage sites in glycoproteins using bio-basis function neural networks"
    • Z. R. Yang and K. C. Chou, "Predicting the O-linkage sites in glycoproteins using bio-basis function neural networks," Bioinformat., vol. 20, pp. 903-908, 2004.
    • (2004) Bioinformat. , vol.20 , pp. 903-908
    • Yang, Z.R.1    Chou, K.C.2
  • 41
    • 0345293243 scopus 로고    scopus 로고
    • "Extracting decision rules from protein sequences using genetic programming methods"
    • Z. R. Yang, R. Thomson, C. Hodgman, and A. K. Doyle, "Extracting decision rules from protein sequences using genetic programming methods," BioSystems, vol. 72, pp. 159-176, 2003.
    • (2003) BioSystems , vol.72 , pp. 159-176
    • Yang, Z.R.1    Thomson, R.2    Hodgman, C.3    Doyle, A.K.4
  • 42
    • 13844272392 scopus 로고    scopus 로고
    • "Bio-basis function neural network for prediction of protease cleavage sites in proteins"
    • to be published
    • Z. R. Yang and R. Thomson, "Bio-basis function neural network for prediction of protease cleavage sites in proteins," IEEE Trans Neural Netw., to be published.
    • IEEE Trans Neural Netw.
    • Yang, Z.R.1    Thomson, R.2
  • 43
    • 13644264642 scopus 로고    scopus 로고
    • "Reduced bio-basis function neural networks for protease cleavage site prediction"
    • to be published
    • Z. R. Yang and E. Berry, "Reduced bio-basis function neural networks for protease cleavage site prediction," J. Computat. Biol. Bioinformat., to be published.
    • J. Computat. Biol. Bioinformat.
    • Yang, Z.R.1    Berry, E.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.