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Volumn 8, Issue 4, 2013, Pages

Conformational B-Cell Epitope Prediction on Antigen Protein Structures: A Review of Current Algorithms and Comparison with Common Binding Site Prediction Methods

Author keywords

[No Author keywords available]

Indexed keywords

EPITOPE;

EID: 84876426871     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0062249     Document Type: Article
Times cited : (108)

References (29)
  • 1
    • 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 JM, Guo D, Hodges RS, (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 25: 5425-5432.
    • (1986) Biochemistry , vol.25 , pp. 5425-5432
    • Parker, J.M.1    Guo, D.2    Hodges, R.S.3
  • 2
    • 0022249654 scopus 로고
    • Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide
    • Emini EA, Hughes JV, Perlow DS, Boger J, (1985) Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide. J Virol 55: 836-839.
    • (1985) J Virol , vol.55 , pp. 836-839
    • Emini, E.A.1    Hughes, J.V.2    Perlow, D.S.3    Boger, J.4
  • 3
    • 0021918946 scopus 로고
    • Prediction of Chain Flexibility in Proteins - a Tool for the Selection of Peptide Antigens
    • Karplus PA, Schulz GE, (1985) Prediction of Chain Flexibility in Proteins- a Tool for the Selection of Peptide Antigens. Naturwissenschaften 72: 212-213.
    • (1985) Naturwissenschaften , vol.72 , pp. 212-213
    • Karplus, P.A.1    Schulz, G.E.2
  • 4
    • 0025605617 scopus 로고
    • A semi-empirical method for prediction of antigenic determinants on protein antigens
    • Kolaskar AS, Tongaonkar PC, (1990) A semi-empirical method for prediction of antigenic determinants on protein antigens. FEBS Lett 276: 172-174.
    • (1990) FEBS Lett , vol.276 , pp. 172-174
    • Kolaskar, A.S.1    Tongaonkar, P.C.2
  • 5
    • 33751104704 scopus 로고    scopus 로고
    • Improved method for predicting linear B-cell epitopes
    • Larsen JE, Lund O, Nielsen M, (2006) Improved method for predicting linear B-cell epitopes. Immunome Res 2: 2.
    • (2006) Immunome Res , vol.2 , pp. 2
    • Larsen, J.E.1    Lund, O.2    Nielsen, M.3
  • 6
    • 33748254730 scopus 로고    scopus 로고
    • Prediction of continuous B-cell epitopes in an antigen using recurrent neural network
    • Saha S, Raghava GP, (2006) Prediction of continuous B-cell epitopes in an antigen using recurrent neural network. Proteins 65: 40-48.
    • (2006) Proteins , vol.65 , pp. 40-48
    • Saha, S.1    Raghava, G.P.2
  • 7
    • 34548301416 scopus 로고    scopus 로고
    • Prediction of linear B-cell epitopes using amino acid pair antigenicity scale
    • Chen J, Liu H, Yang J, Chou KC, (2007) Prediction of linear B-cell epitopes using amino acid pair antigenicity scale. Amino Acids 33: 423-428.
    • (2007) Amino Acids , vol.33 , pp. 423-428
    • Chen, J.1    Liu, H.2    Yang, J.3    Chou, K.C.4
  • 8
    • 47649130438 scopus 로고    scopus 로고
    • Predicting linear B-cell epitopes using string kernels
    • El-Manzalawy Y, Dobbs D, Honavar V, (2008) Predicting linear B-cell epitopes using string kernels. J Mol Recognit 21: 243-255.
    • (2008) J Mol Recognit , vol.21 , pp. 243-255
    • El-Manzalawy, Y.1    Dobbs, D.2    Honavar, V.3
  • 9
    • 11144246404 scopus 로고    scopus 로고
    • Benchmarking B cell epitope prediction: underperformance of existing methods
    • Blythe MJ, Flower DR, (2005) Benchmarking B cell epitope prediction: underperformance of existing methods. Protein Sci 14: 246-248.
    • (2005) Protein Sci , vol.14 , pp. 246-248
    • Blythe, M.J.1    Flower, D.R.2
  • 10
    • 34248581488 scopus 로고    scopus 로고
    • Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools
    • Greenbaum JA, Andersen PH, Blythe M, Bui HH, Cachau RE, et al. (2007) Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools. J Mol Recognit 20: 75-82.
    • (2007) J Mol Recognit , vol.20 , pp. 75-82
    • Greenbaum, J.A.1    Andersen, P.H.2    Blythe, M.3    Bui, H.H.4    Cachau, R.E.5
  • 11
    • 60749128663 scopus 로고    scopus 로고
    • COBEpro: a novel system for predicting continuous B-cell epitopes
    • Sweredoski MJ, Baldi P, (2009) COBEpro: a novel system for predicting continuous B-cell epitopes. Protein Eng Des Sel 22: 113-120.
    • (2009) Protein Eng Des Sel , vol.22 , pp. 113-120
    • Sweredoski, M.J.1    Baldi, P.2
  • 12
    • 64049090391 scopus 로고    scopus 로고
    • An introduction to epitope prediction methods and software
    • Yang X, Yu X, (2009) An introduction to epitope prediction methods and software. Rev Med Virol 19: 77-96.
    • (2009) Rev Med Virol , vol.19 , pp. 77-96
    • Yang, X.1    Yu, X.2
  • 13
    • 0030174309 scopus 로고    scopus 로고
    • Mapping Epitope Structure and Activity: From One-Dimensional Prediction to Four-Dimensional Description of Antigenic Specificity
    • Van Regenmortel MHV, (1996) Mapping Epitope Structure and Activity: From One-Dimensional Prediction to Four-Dimensional Description of Antigenic Specificity. Methods 9: 465-472.
    • (1996) Methods , vol.9 , pp. 465-472
    • Van Regenmortel, M.H.V.1
  • 15
    • 33751099863 scopus 로고    scopus 로고
    • Prediction of residues in discontinuous B-cell epitopes using protein 3D structures
    • Andersen PH, Nielsen M, Lund O, (2006) Prediction of residues in discontinuous B-cell epitopes using protein 3D structures. Protein Science 15: 2558-2567.
    • (2006) Protein Science , vol.15 , pp. 2558-2567
    • Andersen, P.H.1    Nielsen, M.2    Lund, O.3
  • 16
    • 45449086674 scopus 로고    scopus 로고
    • PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure
    • Sweredoski MJ, Baldi P, (2008) PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure. Bioinformatics 24: 1459-1460.
    • (2008) Bioinformatics , vol.24 , pp. 1459-1460
    • Sweredoski, M.J.1    Baldi, P.2
  • 17
  • 18
    • 67849086859 scopus 로고    scopus 로고
    • SEPPA: a computational server for spatial epitope prediction of protein antigens
    • Sun J, Wu D, Xu T, Wang X, Xu X, et al. (2009) SEPPA: a computational server for spatial epitope prediction of protein antigens. Nucleic Acids Res 37: W612-616.
    • (2009) Nucleic Acids Res , vol.37
    • Sun, J.1    Wu, D.2    Xu, T.3    Wang, X.4    Xu, X.5
  • 19
    • 59249095901 scopus 로고    scopus 로고
    • A machine-learning approach for predicting B-cell epitopes
    • Rubinstein ND, Mayrose I, Pupko T, (2009) A machine-learning approach for predicting B-cell epitopes. Mol Immunol 46: 840-847.
    • (2009) Mol Immunol , vol.46 , pp. 840-847
    • Rubinstein, N.D.1    Mayrose, I.2    Pupko, T.3
  • 21
    • 70449408296 scopus 로고    scopus 로고
    • Prediction of antigenic epitopes on protein surfaces by consensus scoring
    • Liang S, Zheng D, Zhang C, Zacharias M, (2009) Prediction of antigenic epitopes on protein surfaces by consensus scoring. BMC bioinformatics 10: 302.
    • (2009) BMC Bioinformatics , vol.10 , pp. 302
    • Liang, S.1    Zheng, D.2    Zhang, C.3    Zacharias, M.4
  • 22
    • 77954543849 scopus 로고    scopus 로고
    • EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results
    • Liang S, Zheng D, Standley DM, Yao B, Zacharias M, et al. (2010) EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results. BMC bioinformatics 11: 381.
    • (2010) BMC Bioinformatics , vol.11 , pp. 381
    • Liang, S.1    Zheng, D.2    Standley, D.M.3    Yao, B.4    Zacharias, M.5
  • 23
    • 80051623308 scopus 로고    scopus 로고
    • Prediction of conformational B-cell epitopes from 3D structures by random forests with a distance-based feature
    • Zhang W, Xiong Y, Zhao M, Zou H, Ye X, et al. (2011) Prediction of conformational B-cell epitopes from 3D structures by random forests with a distance-based feature. BMC bioinformatics 12: 341.
    • (2011) BMC Bioinformatics , vol.12 , pp. 341
    • Zhang, W.1    Xiong, Y.2    Zhao, M.3    Zou, H.4    Ye, X.5
  • 24
    • 37749042370 scopus 로고    scopus 로고
    • Antibody-protein interactions: benchmark datasets and prediction tools evaluation
    • Ponomarenko JV, Bourne PE, (2007) Antibody-protein interactions: benchmark datasets and prediction tools evaluation. BMC Struct Biol 7: 64.
    • (2007) BMC Struct Biol , vol.7 , pp. 64
    • Ponomarenko, J.V.1    Bourne, P.E.2
  • 25
    • 78149293634 scopus 로고    scopus 로고
    • Recent advances in B-cell epitope prediction methods
    • El-Manzalawy Y, Honavar V, (2010) Recent advances in B-cell epitope prediction methods. Immunome research 6 (Suppl 2):: S2.
    • (2010) Immunome Research , vol.6 , Issue.SUPPL. 2
    • El-Manzalawy, Y.1    Honavar, V.2
  • 26
    • 1842526090 scopus 로고    scopus 로고
    • ProMate: a structure based prediction program to identify the location of protein-protein binding sites
    • Neuvirth H, Raz R, Schreiber G, (2004) ProMate: a structure based prediction program to identify the location of protein-protein binding sites. Journal of molecular biology 338: 181-199.
    • (2004) Journal of Molecular Biology , vol.338 , pp. 181-199
    • Neuvirth, H.1    Raz, R.2    Schreiber, G.3
  • 27
    • 77954257799 scopus 로고    scopus 로고
    • ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids
    • Ashkenazy H, Erez E, Martz E, Pupko T, Ben-Tal N, (2010) ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic acids research 38: W529-533.
    • (2010) Nucleic Acids Research , vol.38
    • Ashkenazy, H.1    Erez, E.2    Martz, E.3    Pupko, T.4    Ben-Tal, N.5
  • 28
    • 33747150197 scopus 로고    scopus 로고
    • Protein binding site prediction using an empirical scoring function
    • Liang S, Zhang C, Liu S, Zhou Y, (2006) Protein binding site prediction using an empirical scoring function. Nucleic acids research 34: 3698-3707.
    • (2006) Nucleic Acids Research , vol.34 , pp. 3698-3707
    • Liang, S.1    Zhang, C.2    Liu, S.3    Zhou, Y.4
  • 29
    • 33947360625 scopus 로고    scopus 로고
    • PIER: protein interface recognition for structural proteomics
    • Kufareva I, Budagyan L, Raush E, Totrov M, Abagyan R, (2007) PIER: protein interface recognition for structural proteomics. Proteins 67: 400-417.
    • (2007) Proteins , vol.67 , pp. 400-417
    • Kufareva, I.1    Budagyan, L.2    Raush, E.3    Totrov, M.4    Abagyan, R.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.