메뉴 건너뛰기




Volumn 6, Issue 5, 2012, Pages 557-569

Predicting linear B-cell epitopes by using sequence-derived structural and physicochemical features

Author keywords

Feature selection; Linear B cell epitopes; Sequence derived structural and physicochemical features; Support vector machine; SVM

Indexed keywords


EID: 84867094249     PISSN: 17485673     EISSN: 17485681     Source Type: Journal    
DOI: 10.1504/IJDMB.2012.049298     Document Type: Article
Times cited : (25)

References (42)
  • 1
    • 0032829397 scopus 로고    scopus 로고
    • Predictive estimation of protein linear epitopes by using the program PEOPLE
    • Alix, A.J. (1999) 'Predictive estimation of protein linear epitopes by using the program PEOPLE', Vaccine, Vol. 18, Nos. 3-4, pp.311-314.
    • (1999) Vaccine , vol.18 , Issue.3-4 , pp. 311-314
    • Alix, A.J.1
  • 2
    • 2542458612 scopus 로고    scopus 로고
    • Classification of nuclear receptors based on amino acid composition and dipeptide composition
    • Bhasin, M. and Raghava, G.P.S. (2004) 'Classification of nuclear receptors based on amino acid composition and dipeptide composition', J. Bio. Chem., Vol. 279, p.23262.
    • (2004) J. Bio. Chem. , vol.279 , pp. 23262
    • Bhasin, M.1    Raghava, G.P.S.2
  • 3
    • 11144246404 scopus 로고    scopus 로고
    • Benchmarking B cell epitope prediction: Underperformance of existing methods
    • Blythe, M.J. and Flower, D.R. (2005) 'Benchmarking B cell epitope prediction: underperformance of existing methods', Protein Sci., Vol. 14, No. 1, pp.246-248.
    • (2005) Protein Sci. , vol.14 , Issue.1 , pp. 246-248
    • Blythe, M.J.1    Flower, D.R.2
  • 5
    • 34548301416 scopus 로고    scopus 로고
    • Prediction of linear B-cell epitopes using amino acid pair antigenicity scale
    • Chen, J., Liu, H., Yang, J. and Chou, K. (2007) 'Prediction of linear B-cell epitopes using amino acid pair antigenicity scale', Amino Acids, Vol. 33, No. 3, pp.423-428.
    • (2007) Amino Acids , vol.33 , Issue.3 , pp. 423-428
    • Chen, J.1    Liu, H.2    Yang, J.3    Chou, K.4
  • 6
    • 0034687538 scopus 로고    scopus 로고
    • Prediction of protein subcellar locations by incorporating quasi-sequence-order effect
    • Chou, K.C. (2000) 'Prediction of protein subcellar locations by incorporating quasi-sequence-order effect', Biochemical and Biophysical Research Communications, Vol. 278, pp.477-483.
    • (2000) Biochemical and Biophysical Research Communications , vol.278 , pp. 477-483
    • Chou, K.C.1
  • 7
    • 3142779931 scopus 로고    scopus 로고
    • Prediction of protein sucellular locations by GO-FunD-PseAA predictor
    • Chou, K.C. and Cai, Y. (2004) 'Prediction of protein sucellular locations by GO-FunD-PseAA predictor', Biochemical and Biophysical Research Communications, Vol. 320, pp.1236-1239.
    • (2004) Biochemical and Biophysical Research Communications , vol.320 , pp. 1236-1239
    • Chou, K.C.1    Cai, Y.2
  • 9
    • 84960463485 scopus 로고    scopus 로고
    • Minimum redundancy feature selection from microarray gene expression data
    • 11-14 August, Stanford, CA, USA
    • Ding, C. and Peng, H.C. (2003) 'Minimum redundancy feature selection from microarray gene expression data', 2nd IEEE Computer Society Bioinformatics Conference (CSB 2003), 11-14 August, Stanford, CA, USA, pp.523-529.
    • (2003) 2nd IEEE Computer Society Bioinformatics Conference (CSB 2003) , pp. 523-529
    • Ding, C.1    Peng, H.C.2
  • 10
    • 0029047319 scopus 로고
    • Prediction of protein folding class using global description of amino acid sequence
    • Dubchak, I., Muchink, I., Holbrook, R.S. and Kim, S.H. (1995) 'Prediction of protein folding class using global description of amino acid sequence', Proc. Natl. Acad. Sci. USA, Vol. 92, pp.8700-8704.
    • (1995) Proc. Natl. Acad. Sci. USA , vol.92 , pp. 8700-8704
    • Dubchak, I.1    Muchink, I.2    Holbrook, R.S.3    Kim, S.H.4
  • 12
    • 47649130438 scopus 로고    scopus 로고
    • Predicting linear B-cell epitopes using string kernels
    • El-Manzalawy, Y., Dobbs, D. and Honavar, V. (2008) 'Predicting linear B-cell epitopes using string kernels', J. Mol. Recognit., Vol. 21, No. 4, pp.243-255.
    • (2008) J. Mol. Recognit. , vol.21 , Issue.4 , pp. 243-255
    • El-Manzalawy, Y.1    Dobbs, D.2    Honavar, V.3
  • 13
    • 0022249654 scopus 로고    scopus 로고
    • Induction of hepatitis a virus-neutralizing antibody by a virus-specific synthetic peptide
    • Emini, E.A., Hughes, J.V., Perlow, D.S. and Boger, J. (1998) 'Induction of hepatitis a virus-neutralizing antibody by a virus-specific synthetic peptide', J. Virol., Vol. 55, No. 3, pp.836-839.
    • (1998) J. Virol. , vol.55 , Issue.3 , pp. 836-839
    • Emini, E.A.1    Hughes, J.V.2    Perlow, D.S.3    Boger, J.4
  • 15
    • 0000960565 scopus 로고
    • The contiguity ratio and statistical mapping
    • Geary, R.C. (1954) 'The contiguity ratio and statistical mapping', Incorp. Statist., Vol. 5, pp.115-145.
    • (1954) Incorp. Statist. , vol.5 , pp. 115-145
    • Geary, R.C.1
  • 16
    • 0021918946 scopus 로고
    • Prediction of chain flexibility in proteins - A tool for the selection of peptide antigens
    • Karplus, P.A. and Schulz, G.E. (1985) 'Prediction of chain flexibility in proteins - a tool for the selection of peptide antigens', Naturwissenschaften, Vol. 72, pp.212, 213.
    • (1985) Naturwissenschaften , vol.72 , pp. 212-213
    • Karplus, P.A.1    Schulz, G.E.2
  • 17
    • 0025605617 scopus 로고
    • A semi-empirical method for prediction of antigenic determinants on protein antigens
    • Kolaskar, A.S. and Tongaonkar, P.C. (1990) 'A semi-empirical method for prediction of antigenic determinants on protein antigens', FEBS Lett., Vol. 276, Nos. 1-2, pp.172-174.
    • (1990) FEBS Lett. , vol.276 , Issue.1-2 , pp. 172-174
    • Kolaskar, A.S.1    Tongaonkar, P.C.2
  • 18
    • 33751104704 scopus 로고    scopus 로고
    • Improved method for predicting linear B-cell epitopes
    • Larsen, J., Lund, O. and Nielsen, M. (2006) 'Improved method for predicting linear B-cell epitopes', Immun. Res., Vol. 2, p.2.
    • (2006) Immun. Res. , vol.2 , pp. 2
    • Larsen, J.1    Lund, O.2    Nielsen, M.3
  • 19
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences
    • Li, W. and Godzik, A. (2006) 'Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences', Bioinformatics, Vol. 22, pp.1658-1659.
    • (2006) Bioinformatics , vol.22 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 20
    • 76549254593 scopus 로고
    • Notes on continuous stochastic phenomena
    • Moran, P.A.P. (1950) 'Notes on continuous stochastic phenomena', Biometrika, Vol. 37, pp.17-23.
    • (1950) Biometrika , vol.37 , pp. 17-23
    • Moran, P.A.P.1
  • 21
    • 0001486261 scopus 로고
    • Autocorrelation of molecular structures, application to SAR studies
    • Moreau, G. and Broto, P. (1980) 'Autocorrelation of molecular structures, application to SAR studies', Nour J. Chim., Vol. 4, pp.757-767.
    • (1980) Nour J. Chim. , vol.4 , pp. 757-767
    • Moreau, G.1    Broto, P.2
  • 23
    • 0037263777 scopus 로고    scopus 로고
    • BEPITOPE: Predicting the location of continuous epitopes and patterns in proteins
    • Odorico, M. and Pellequer, J.L. (2003) 'BEPITOPE: predicting the location of continuous epitopes and patterns in proteins', J. Mol. Recogn., Vol. 16, No. 1, pp.20-22.
    • (2003) J. Mol. Recogn. , vol.16 , Issue.1 , pp. 20-22
    • Odorico, M.1    Pellequer, J.L.2
  • 24
    • 0023055775 scopus 로고
    • New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data:correlation of predicted surface residues with antigenicity and x-ray derived accessible sites
    • Parker, J.M., Guo, D. and Hodges, R.S. (1986) 'New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data:correlation of predicted surface residues with antigenicity and x-ray derived accessible sites', Biochemistry, Vol. 25, No. 19, pp.5425-5432.
    • (1986) Biochemistry , vol.25 , Issue.19 , pp. 5425-5432
    • Parker, J.M.1    Guo, D.2    Hodges, R.S.3
  • 25
    • 0027656984 scopus 로고
    • PREDITOP. A program for antigenicity prediction
    • Pellequer, J. and Westhof, E. (1993) 'PREDITOP. a program for antigenicity prediction', J. Mol. Graph, Vol. 11, No. 3, pp.204-210.
    • (1993) J. Mol. Graph , vol.11 , Issue.3 , pp. 204-210
    • Pellequer, J.1    Westhof, E.2
  • 26
    • 0026350055 scopus 로고
    • Predicting location of continuous epitopes in proteins from their primary structures
    • Pellequer, J., Westhof, E. and Van Regenmortel, M. (1991) 'Predicting location of continuous epitopes in proteins from their primary structures', Meth. Enzymol., Vol. 203, pp.176-201.
    • (1991) Meth. Enzymol. , vol.203 , pp. 176-201
    • Pellequer, J.1    Westhof, E.2    Van Regenmortel, M.3
  • 27
    • 0027156564 scopus 로고
    • Correlation between the location of antigenic sites and the prediction of turns in proteins
    • Pellequer, J., Westhof, E. and Van Regenmortel, M. (1993) 'Correlation between the location of antigenic sites and the prediction of turns in proteins', Immunol. Lett., Vol. 36, No. 1, pp.83-99.
    • (1993) Immunol. Lett. , vol.36 , Issue.1 , pp. 83-99
    • Pellequer, J.1    Westhof, E.2    Van Regenmortel, M.3
  • 28
    • 24344458137 scopus 로고    scopus 로고
    • Feature selection based on mutual information: Criteria of max-dependency, max-relevance, and min-redundancy
    • Peng, H.C., Long, F. and Ding, C. (2005) 'Feature selection based on mutual information: criteria of max-dependency, max-relevance, and min-redundancy', IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol. 27, No. 8, pp.1226-1238.
    • (2005) IEEE Transactions on Pattern Analysis and Machine Intelligence , vol.27 , Issue.8 , pp. 1226-1238
    • Peng, H.C.1    Long, F.2    Ding, C.3
  • 29
    • 35048872790 scopus 로고    scopus 로고
    • BcePred: Prediction of continuous B-cell epitopes in antigenic sequences using physico-chemical properties
    • Saha, S. and Raghava, G.P. (2004) 'BcePred: prediction of continuous B-cell epitopes in antigenic sequences using physico-chemical properties', Lect. Notes Comput. Sci., Vol. 3239, pp.197-204.
    • (2004) Lect. Notes Comput. Sci. , vol.3239 , pp. 197-204
    • Saha, S.1    Raghava, G.P.2
  • 30
    • 33748254730 scopus 로고    scopus 로고
    • Prediction of continuous B-cell epitopes in an antigen using recurrent neural network
    • Saha, S. and Raghava, G.P. (2006) 'Prediction of continuous B-cell epitopes in an antigen using recurrent neural network', Proteins, Vol. 65, No. 1, pp.40-48.
    • (2006) Proteins , vol.65 , Issue.1 , pp. 40-48
    • Saha, S.1    Raghava, G.P.2
  • 31
    • 25444509811 scopus 로고    scopus 로고
    • Bcipep: A database of B-cell epitopes
    • Saha, S., Bhasin, M. and Raghava, G.P. (2005) 'Bcipep:A database of B-cell epitopes', BMC Genomics, Vol. 6, No. 1, p.79.
    • (2005) BMC Genomics , vol.6 , Issue.1 , pp. 79
    • Saha, S.1    Bhasin, M.2    Raghava, G.P.3
  • 32
  • 33
    • 33745030152 scopus 로고    scopus 로고
    • Machine learning approaches for prediction of linear B-cell epitopes on proteins
    • Sollner, J. and Mayer, B. (2006) 'Machine learning approaches for prediction of linear B-cell epitopes on proteins', J. Mol. Recogn., Vol. 19, No. 3, pp.200-208.
    • (2006) J. Mol. Recogn. , vol.19 , Issue.3 , pp. 200-208
    • Sollner, J.1    Mayer, B.2
  • 34
    • 60749128663 scopus 로고    scopus 로고
    • COBEpro: A novel system for predicting continuous B-cell epitopes
    • Sweredoski, M.J. and Baldi, P. (2009) 'COBEpro: a novel system for predicting continuous B-cell epitopes', Protein Eng. Des. Sel., Vol. 22, No. 3, pp.113-120.
    • (2009) Protein Eng. Des. Sel. , vol.22 , Issue.3 , pp. 113-120
    • Sweredoski, M.J.1    Baldi, P.2
  • 35
    • 0024967840 scopus 로고
    • The concept and operational definition of protein epitopes
    • Van Regenmortel, M.H. (1989) 'The concept and operational definition of protein epitopes', Philos Trans. R. Soc. Lond. B. Biol. Sci., Vol. 323, No. 1217, pp.451-466.
    • (1989) Philos Trans. R. Soc. Lond. B. Biol. Sci. , vol.323 , Issue.1217 , pp. 451-466
    • Van Regenmortel, M.H.1
  • 36
    • 0035925606 scopus 로고    scopus 로고
    • Pitfalls of reductionism in the design of peptide-cased vaccines
    • Van Regenmortel, M.H. (2004) 'Pitfalls of reductionism in the design of peptide-cased vaccines', Vaccine, Vol. 19, pp.2369-2374.
    • (2004) Vaccine , vol.19 , pp. 2369-2374
    • Van Regenmortel, M.H.1
  • 38
    • 0022621996 scopus 로고
    • Production and use of antibodies against synthetic peptides
    • Walter, G. (1986) 'Production and use of antibodies against synthetic peptides', J. Immunol. Methods, Vol. 88, No. 2, pp.149-161.
    • (1986) J. Immunol. Methods , vol.88 , Issue.2 , pp. 149-161
    • Walter, G.1
  • 39
    • 2542507623 scopus 로고    scopus 로고
    • Peptide vaccines and peptide libraries
    • Wiesmuller, K.H., Fleckenstein, B. and Jung, G. (2001) 'Peptide vaccines and peptide libraries', Biol. Chem., Vol. 382, No. 4, pp.571-579.
    • (2001) Biol. Chem. , vol.382 , Issue.4 , pp. 571-579
    • Wiesmuller, K.H.1    Fleckenstein, B.2    Jung, G.3
  • 40
    • 65549170702 scopus 로고    scopus 로고
    • Feature cluster selection for high-throughput data analysis
    • Yu, L. (2009) 'Feature cluster selection for high-throughput data analysis', International Journal of Data Mining and Bioinformatics, Vol. 3, No. 2, pp.177-191.
    • (2009) International Journal of Data Mining and Bioinformatics , vol.3 , Issue.2 , pp. 177-191
    • Yu, L.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.