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Volumn 11, Issue , 2015, Pages 98-102

Antibody specific epitope prediction - Emergence of a new paradigm

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBODY; EPITOPE; IMMUNOGLOBULIN; VIRUS ANTIGEN;

EID: 84926005823     PISSN: 18796257     EISSN: 18796265     Source Type: Journal    
DOI: 10.1016/j.coviro.2015.03.012     Document Type: Review
Times cited : (65)

References (51)
  • 1
    • 77954521521 scopus 로고    scopus 로고
    • Evaluation of spatial epitope computational tools based on experimentally-confirmed dataset for protein antigens
    • X. Xu, J. Sun, Q. Liu, X. Wang, T. Xu, R. Zhu, D. Wu, and X. Cao Evaluation of spatial epitope computational tools based on experimentally-confirmed dataset for protein antigens Chin Sci Bull 55 2010 2169 2174
    • (2010) Chin Sci Bull , vol.55 , pp. 2169-2174
    • Xu, X.1    Sun, J.2    Liu, Q.3    Wang, X.4    Xu, T.5    Zhu, R.6    Wu, D.7    Cao, X.8
  • 3
    • 33746456834 scopus 로고    scopus 로고
    • CED: A conformational epitope database
    • J. Huang, and W. Honda CED: a conformational epitope database BMC Immunol 7 2006 7
    • (2006) BMC Immunol , vol.7 , pp. 7
    • Huang, J.1    Honda, W.2
  • 4
    • 78149293634 scopus 로고    scopus 로고
    • Recent advances in B-cell epitope prediction methods
    • Y. El-Manzalawy, and V. Honavar Recent advances in B-cell epitope prediction methods Immunome Res 6 Suppl. 2 2010 S2
    • (2010) Immunome Res , vol.6 , pp. S2
    • El-Manzalawy, Y.1    Honavar, V.2
  • 5
    • 0000448982 scopus 로고
    • Prediction of protein antigenic determinants from amino acid sequences
    • T.P. Hopp, and K.R. Woods Prediction of protein antigenic determinants from amino acid sequences Proc Natl Acad Sci USA 78 1981 3824 3828
    • (1981) Proc Natl Acad Sci USA , vol.78 , pp. 3824-3828
    • Hopp, T.P.1    Woods, K.R.2
  • 6
    • 0025605617 scopus 로고
    • A semi-empirical method for prediction of antigenic determinants on protein antigens
    • A.S. Kolaskar, and P.C. Tongaonkar A semi-empirical method for prediction of antigenic determinants on protein antigens FEBS Lett 276 1990 172 174
    • (1990) FEBS Lett , vol.276 , pp. 172-174
    • Kolaskar, A.S.1    Tongaonkar, P.C.2
  • 7
    • 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
    • J.M. Parker, D. Guo, and R.S. Hodges 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 1986 5425 5432
    • (1986) Biochemistry , vol.25 , pp. 5425-5432
    • Parker, J.M.1    Guo, D.2    Hodges, R.S.3
  • 8
    • 0026350055 scopus 로고
    • Predicting location of continuous epitopes in proteins from their primary structures
    • J.L. Pellequer, E. Westhof, and M.H. Van Regenmortel Predicting location of continuous epitopes in proteins from their primary structures Methods Enzymol 203 1991 176 201
    • (1991) Methods Enzymol , vol.203 , pp. 176-201
    • Pellequer, J.L.1    Westhof, E.2    Van Regenmortel, M.H.3
  • 10
    • 0027156564 scopus 로고
    • Correlation between the location of antigenic sites and the prediction of turns in proteins
    • J.L. Pellequer, E. Westhof, and M.H. Van Regenmortel Correlation between the location of antigenic sites and the prediction of turns in proteins Immunol Lett 36 1993 83 99
    • (1993) Immunol Lett , vol.36 , pp. 83-99
    • Pellequer, J.L.1    Westhof, E.2    Van Regenmortel, M.H.3
  • 11
    • 0027656984 scopus 로고
    • PREDITOP: A program for antigenicity prediction
    • 191-202
    • J.L. Pellequer, and E. Westhof PREDITOP: a program for antigenicity prediction J Mol Graph 11 1993 204 210 191-202
    • (1993) J Mol Graph , vol.11 , pp. 204-210
    • Pellequer, J.L.1    Westhof, E.2
  • 12
    • 0032829397 scopus 로고    scopus 로고
    • Predictive estimation of protein linear epitopes by using the program PEOPLE
    • A.J. Alix Predictive estimation of protein linear epitopes by using the program PEOPLE Vaccine 18 1999 311 314
    • (1999) Vaccine , vol.18 , pp. 311-314
    • Alix, A.J.1
  • 13
    • 0037263777 scopus 로고    scopus 로고
    • BEPITOPE: Predicting the location of continuous epitopes and patterns in proteins
    • M. Odorico, and J.L. Pellequer BEPITOPE: predicting the location of continuous epitopes and patterns in proteins J Mol Recognit 16 2003 20 22
    • (2003) J Mol Recognit , vol.16 , pp. 20-22
    • Odorico, M.1    Pellequer, J.L.2
  • 14
    • 11144246404 scopus 로고    scopus 로고
    • Benchmarking B cell epitope prediction: Underperformance of existing methods
    • M.J. Blythe, and D.R. Flower Benchmarking B cell epitope prediction: underperformance of existing methods Protein Sci 14 2005 246 248
    • (2005) Protein Sci , vol.14 , pp. 246-248
    • Blythe, M.J.1    Flower, D.R.2
  • 15
    • 84925884639 scopus 로고    scopus 로고
    • Computational prediction of B cell epitopes from antigen sequences
    • J. Gao, and L. Kurgan Computational prediction of B cell epitopes from antigen sequences Methods Mol Biol 1184 2014 197 215
    • (2014) Methods Mol Biol , vol.1184 , pp. 197-215
    • Gao, J.1    Kurgan, L.2
  • 17
    • 84872049601 scopus 로고    scopus 로고
    • Reliable B cell epitope predictions: Impacts of method development and improved benchmarking
    • J.V. Kringelum, C. Lundegaard, O. Lund, and M. Nielsen Reliable B cell epitope predictions: impacts of method development and improved benchmarking PLoS Comput Biol 8 2012 e1002829
    • (2012) PLoS Comput Biol , vol.8 , pp. e1002829
    • Kringelum, J.V.1    Lundegaard, C.2    Lund, O.3    Nielsen, M.4
  • 18
    • 37749042370 scopus 로고    scopus 로고
    • Antibody-protein interactions: Benchmark datasets and prediction tools evaluation
    • J.V. Ponomarenko, and P.E. Bourne Antibody-protein interactions: benchmark datasets and prediction tools evaluation BMC Struct Biol 7 2007
    • (2007) BMC Struct Biol , vol.7
    • Ponomarenko, J.V.1    Bourne, P.E.2
  • 19
    • 84877137566 scopus 로고    scopus 로고
    • Evaluation and use of in-silico structure-based epitope prediction with foot-and-mouth disease virus
    • D.W. Borley, M. Mahapatra, D.J. Paton, R.M. Esnouf, D.I. Stuart, and E.E. Fry Evaluation and use of in-silico structure-based epitope prediction with foot-and-mouth disease virus PLoS One 8 2013 e61122
    • (2013) PLoS One , vol.8 , pp. e61122
    • Borley, D.W.1    Mahapatra, M.2    Paton, D.J.3    Esnouf, R.M.4    Stuart, D.I.5    Fry, E.E.6
  • 20
    • 84876426871 scopus 로고    scopus 로고
    • Conformational B-cell epitope prediction on antigen protein structures: A review of current algorithms and comparison with common binding site prediction methods
    • B. Yao, D. Zheng, S. Liang, and C. Zhang Conformational B-cell epitope prediction on antigen protein structures: a review of current algorithms and comparison with common binding site prediction methods PLoS One 8 2013 e62249
    • (2013) PLoS One , vol.8 , pp. e62249
    • Yao, B.1    Zheng, D.2    Liang, S.3    Zhang, C.4
  • 22
    • 64049090391 scopus 로고    scopus 로고
    • An introduction to epitope prediction methods and software
    • X.D. Yang, and X.L. Yu An introduction to epitope prediction methods and software Rev Med Virol 19 2009 77 96
    • (2009) Rev Med Virol , vol.19 , pp. 77-96
    • Yang, X.D.1    Yu, X.L.2
  • 23
    • 84925884513 scopus 로고    scopus 로고
    • Prediction of conformational B-cell epitopes
    • W. Zhang, Y. Niu, Y. Xiong, and M. Ke Prediction of conformational B-cell epitopes Methods Mol Biol 1184 2014 185 196
    • (2014) Methods Mol Biol , vol.1184 , pp. 185-196
    • Zhang, W.1    Niu, Y.2    Xiong, Y.3    Ke, M.4
  • 26
    • 0022668738 scopus 로고
    • Location of 'continuous' antigenic determinants in the protruding regions of proteins
    • J.M. Thornton, M.S. Edwards, W.R. Taylor, and D.J. Barlow Location of 'continuous' antigenic determinants in the protruding regions of proteins EMBO J 5 1986 409 413
    • (1986) EMBO J , vol.5 , pp. 409-413
    • Thornton, J.M.1    Edwards, M.S.2    Taylor, W.R.3    Barlow, D.J.4
  • 27
    • 84885405356 scopus 로고    scopus 로고
    • The structural basis of antibody-antigen recognition
    • I. Sela-Culang, V. Kunik, and Y. Ofran The structural basis of antibody-antigen recognition Front Immunol 4 2013 302
    • (2013) Front Immunol , vol.4 , pp. 302
    • Sela-Culang, I.1    Kunik, V.2    Ofran, Y.3
  • 28
    • 84907940987 scopus 로고    scopus 로고
    • Specificity, polyspecificity, and heterospecificity of antibody-antigen recognition
    • M.H. Van Regenmortel Specificity, polyspecificity, and heterospecificity of antibody-antigen recognition J Mol Recognit 27 2014 627 639
    • (2014) J Mol Recognit , vol.27 , pp. 627-639
    • Van Regenmortel, M.H.1
  • 29
    • 84885006229 scopus 로고    scopus 로고
    • The indistinguishability of epitopes from protein surface is explained by the distinct binding preferences of each of the six antigen-binding loops
    • V. Kunik, and Y. Ofran The indistinguishability of epitopes from protein surface is explained by the distinct binding preferences of each of the six antigen-binding loops Protein Eng Des Sel 26 2013 599 609
    • (2013) Protein Eng des Sel , vol.26 , pp. 599-609
    • Kunik, V.1    Ofran, Y.2
  • 30
    • 0025123333 scopus 로고
    • The structure of protein-protein recognition sites
    • J. Janin, and C. Chothia The structure of protein-protein recognition sites J Biol Chem 265 1990 16027 16030
    • (1990) J Biol Chem , vol.265 , pp. 16027-16030
    • Janin, J.1    Chothia, C.2
  • 31
    • 84863516670 scopus 로고    scopus 로고
    • Structural analysis of B-cell epitopes in antibody:protein complexes
    • J.V. Kringelum, M. Nielsen, S.B. Padkjær, and O. Lund Structural analysis of B-cell epitopes in antibody:protein complexes Mol Immunol 53 2013 24 34
    • (2013) Mol Immunol , vol.53 , pp. 24-34
    • Kringelum, J.V.1    Nielsen, M.2    Padkjær, S.B.3    Lund, O.4
  • 32
    • 34248594570 scopus 로고    scopus 로고
    • Identification of discontinuous antigenic determinants on proteins based on shape complementarities
    • R. Rapberger, A. Lukas, and B. Mayer Identification of discontinuous antigenic determinants on proteins based on shape complementarities J Mol Recognit 20 2007 113 121
    • (2007) J Mol Recognit , vol.20 , pp. 113-121
    • Rapberger, R.1    Lukas, A.2    Mayer, B.3
  • 33
    • 84897980054 scopus 로고    scopus 로고
    • ZDOCK server: Interactive docking prediction of protein-protein complexes and symmetric multimers
    • B.G. Pierce, K. Wiehe, H. Hwang, B.H. Kim, T. Vreven, and Z. Weng ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers Bioinformatics 30 2014 1771 1773
    • (2014) Bioinformatics , vol.30 , pp. 1771-1773
    • Pierce, B.G.1    Wiehe, K.2    Hwang, H.3    Kim, B.H.4    Vreven, T.5    Weng, Z.6
  • 35
    • 21644458102 scopus 로고    scopus 로고
    • Classification of protein complexes based on docking difficulty
    • S. Vajda Classification of protein complexes based on docking difficulty Proteins 60 2005 176 180
    • (2005) Proteins , vol.60 , pp. 176-180
    • Vajda, S.1
  • 36
    • 76749153896 scopus 로고    scopus 로고
    • SnugDock: Paratope structural optimization during antibody-antigen docking compensates for errors in antibody homology models
    • A. Sircar, and J.J. Gray SnugDock: paratope structural optimization during antibody-antigen docking compensates for errors in antibody homology models PLoS Comput Biol 6 2010
    • (2010) PLoS Comput Biol , vol.6
    • Sircar, A.1    Gray, J.J.2
  • 37
    • 48449105393 scopus 로고    scopus 로고
    • The RosettaDock server for local protein-protein docking
    • S. Lyskov, and J.J. Gray The RosettaDock server for local protein-protein docking Nucleic Acids Res 36 2008 W233 W238
    • (2008) Nucleic Acids Res , vol.36 , pp. W233-W238
    • Lyskov, S.1    Gray, J.J.2
  • 38
    • 77955213210 scopus 로고    scopus 로고
    • Use of amino acid composition to predict epitope residues of individual antibodies
    • S. Soga, D. Kuroda, H. Shirai, M. Kobori, and N. Hirayama Use of amino acid composition to predict epitope residues of individual antibodies Protein Eng Des Sel 23 2010 441 448
    • (2010) Protein Eng des Sel , vol.23 , pp. 441-448
    • Soga, S.1    Kuroda, D.2    Shirai, H.3    Kobori, M.4    Hirayama, N.5
  • 40
    • 84906235282 scopus 로고    scopus 로고
    • Improving B-cell epitope prediction and its application to global antibody-antigen docking
    • K. Krawczyk, X. Liu, T. Baker, J. Shi, and C.M. Deane Improving B-cell epitope prediction and its application to global antibody-antigen docking Bioinformatics 30 2014 2288 2294
    • (2014) Bioinformatics , vol.30 , pp. 2288-2294
    • Krawczyk, K.1    Liu, X.2    Baker, T.3    Shi, J.4    Deane, C.M.5
  • 41
    • 84868584302 scopus 로고    scopus 로고
    • A systematic comparison of free and bound antibodies reveals binding-related conformational changes
    • I. Sela-Culang, S. Alon, and Y. Ofran A systematic comparison of free and bound antibodies reveals binding-related conformational changes J Immunol 189 2012 4890 4899
    • (2012) J Immunol , vol.189 , pp. 4890-4899
    • Sela-Culang, I.1    Alon, S.2    Ofran, Y.3
  • 42
    • 67849111558 scopus 로고    scopus 로고
    • RosettaAntibody: Antibody variable region homology modeling server
    • A. Sircar, E.T. Kim, and J.J. Gray RosettaAntibody: antibody variable region homology modeling server Nucleic Acids Res 37 2009 W474 W479
    • (2009) Nucleic Acids Res , vol.37 , pp. W474-W479
    • Sircar, A.1    Kim, E.T.2    Gray, J.J.3
  • 43
    • 84911483076 scopus 로고    scopus 로고
    • Antibody structural modeling with prediction of immunoglobulin structure (PIGS)
    • P. Marcatili, P.P. Olimpieri, A. Chailyan, and A. Tramontano Antibody structural modeling with prediction of immunoglobulin structure (PIGS) Nat Protoc 9 2014 2771 2783
    • (2014) Nat Protoc , vol.9 , pp. 2771-2783
    • Marcatili, P.1    Olimpieri, P.P.2    Chailyan, A.3    Tramontano, A.4
  • 44
    • 77952633690 scopus 로고    scopus 로고
    • Mining for the antibody-antigen interacting associations that predict the B cell epitopes
    • L. Zhao, and J.Y. Li Mining for the antibody-antigen interacting associations that predict the B cell epitopes BMC Struct Biol 10 2010 56
    • (2010) BMC Struct Biol , vol.10 , pp. 56
    • Zhao, L.1    Li, J.Y.2
  • 45
    • 80052890732 scopus 로고    scopus 로고
    • Antibody-specified B-cell epitope prediction in line with the principle of context-awareness
    • L. Zhao, L. Wong, and J.Y. Li Antibody-specified B-cell epitope prediction in line with the principle of context-awareness IEEE-ACM Trans Comput Biol Bioinformat 8 2011 1483 1494
    • (2011) IEEE-ACM Trans Comput Biol Bioinformat , vol.8 , pp. 1483-1494
    • Zhao, L.1    Wong, L.2    Li, J.Y.3
  • 47
    • 84927722994 scopus 로고    scopus 로고
    • PEASE: Predicting B-cell epitopes utilizing antibody sequence
    • I. Sela-Culang, S. Ashkenazi, B. Peters, and Y. Ofran PEASE: predicting B-cell epitopes utilizing antibody sequence Bioinformatics 2014 10.1093/bioinformatics/btu790
    • (2014) Bioinformatics
    • Sela-Culang, I.1    Ashkenazi, S.2    Peters, B.3    Ofran, Y.4
  • 49
    • 77954543849 scopus 로고    scopus 로고
    • EPSVR and EPMeta: Prediction of antigenic epitopes using support vector regression and multiple server results
    • S.D. Liang, D.D. Zheng, D.M. Standley, B. Yao, M. Zacharias, and C. Zhang EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results BMC Bioinformat 11 2010 6
    • (2010) BMC Bioinformat , vol.11 , pp. 6
    • Liang, S.D.1    Zheng, D.D.2    Standley, D.M.3    Yao, B.4    Zacharias, M.5    Zhang, C.6
  • 50
    • 77957984965 scopus 로고    scopus 로고
    • Identification of conformational B-cell epitopes in an antigen from its primary sequence
    • H.R. Ansari, and G.P. Raghava Identification of conformational B-cell epitopes in an antigen from its primary sequence Immunome Res 6 2010 6
    • (2010) Immunome Res , vol.6 , pp. 6
    • Ansari, H.R.1    Raghava, G.P.2


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