Advances in In-silico B-cell Epitope Prediction

Pingping       Sun; Sijia       Guo; Jiahang       Sun; Liming       Tan; Chang       Lu; Zhiqiang       Ma
Abstract

Identification of B-cell epitopes in target antigens is one of the most crucial steps for epitopebased vaccine development, immunodiagnostic tests, antibody production, and disease diagnosis and therapy. Experimental methods for B-cell epitope mapping are time consuming, costly and labor intensive; in the meantime, various in-silico methods are proposed to predict both linear and conformational B-cell epitopes. The accurate identification of B-cell epitopes presents major challenges for immunoinformaticians. In this paper, we have comprehensively reviewed in-silico methods for B-cell epitope identification. The aim of this review is to stimulate the development of better tools which could improve the identification of B-cell epitopes, and further for the development of therapeutic antibodies and diagnostic tools.
Keywords: Epitope prediction, Linear epitope, Conformational epitope, BCR, B-cell, Epitope.
Graphical Abstract

[1] 
Peters, B.; Sidney, J.; Bourne, P.; Bui, H.H.; Buus, S.; Doh, G.; Fleri, W.; Kronenberg, M.; Kubo, R.; Lund, O.; Nemazee, D.; Ponomarenko, J.V.; Sathiamurthy, M.; Schoenberger, S.P.; Stewart, S.; Surko, P.; Way, S.; Wilson, S.; Sette, A. The design and implementation of the immune epitope database and analysis resource. Immunogenetics,  2005, 57(5), 326-336.
[http://dx.doi.org/10.1007/s00251-005-0803-5] [PMID: 15895191] 
[2] 
Van Regenmortel, M.H. The concept and operational definition of protein epitopes. Philos. Trans. R. Soc. Lond. B Biol. Sci.,  1989, 323(1217), 451-466.
[http://dx.doi.org/10.1098/rstb.1989.0023] [PMID: 2474169] 
[3] 
Ponomarenko, J.; Bui, H.H.; Li, W.; Fusseder, N.; Bourne, P.E.; Sette, A.; Peters, B. ElliPro: A new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics,  2008, 9, 514.
[http://dx.doi.org/10.1186/1471-2105-9-514] [PMID: 19055730] 
[4] 
Smith, D.J.; Taubman, M.A.; Holmberg, C.F.; Eastcott, J.; King, W.F.; Ali-Salaam, P. Antigenicity and immunogenicity of a synthetic peptide derived from a glucan-binding domain of mutans streptococcal glucosyltransferase. Infect. Immun.,  1993, 61(7), 2899-2905.
[PMID: 8514393] 
[5] 
Barlow, D.J.; Edwards, M.S.; Thornton, J.M. Continuous and discontinuous protein antigenic determinants. Nature,  1986, 322(6081), 747-748.
[http://dx.doi.org/10.1038/322747a0] [PMID: 2427953] 
[6] 
Castelli, M.; Cappelletti, F.; Diotti, R.A.; Sautto, G.; Criscuolo, E.; Dal Peraro, M.; Clementi, N. Peptide-based vaccinology: experimental and computational approaches to target hypervariable viruses through the fine characterization of protective epitopes recognized by monoclonal antibodies and the identification of T-cell-activating peptides. Clin. Dev. Immunol.,  2013, 2013, 521231.
[http://dx.doi.org/10.1155/2013/521231] [PMID: 23878584] 
[7] 
Rux, J.J.; Burnett, R.M. Type-specific epitope locations revealed by X-ray crystallographic study of adenovirus type 5 hexon. Mol. Ther.,  2000, 1(1), 18-30.
[http://dx.doi.org/ 10.1006/mthe.1999.0001] [PMID: 10933908] 
[8] 
Mayer, M.; Meyer, B. Group epitope mapping by saturation transfer difference NMR to identify segments of a ligand in direct contact with a protein receptor. J. Am. Chem. Soc.,  2001, 123(25), 6108-6117.
[http://dx.doi.org/10.1021/ja0100120] [PMID: 11414845] 
[9] 
Hopp, T.P.; Woods, K.R. Prediction of protein antigenic determinants from amino acid sequences. Proc. Natl. Acad. Sci. USA,  1981, 78(6), 3824-3828.
[http://dx.doi.org/10.1073/pnas.78.6.3824] [PMID: 6167991] 
[10] 
Westhof, E.; Altschuh, D.; Moras, D.; Bloomer, A.C.; Mondragon, A.; Klug, A.; Van Regenmortel, M.H. Correlation between segmental mobility and the location of antigenic determinants in proteins. Nature,  1984, 311(5982), 123-126.
[http://dx.doi.org/ 10.1038/311123a0] [PMID: 6206398] 
[11] 
Emini, E.A.; Hughes, J.V.; Perlow, D.S.; Boger, J. Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide. J. Virol.,  1985, 55(3), 836-839.
[PMID: 2991600] 
[12] 
Karplus, P.A.S.G. Prediction of chain flexibility in proteins - a tool for the selection of peptide antigens. Naturwissenschaften,  1985, 72, 2.
[http://dx.doi.org/10.1007/BF01195768] 
[13] 
Welling, G.W.; Weijer, W.J.; van der Zee, R.; Welling-Wester, S. Prediction of sequential antigenic regions in proteins. FEBS Lett.,  1985, 188(2), 215-218.
[http://dx.doi.org/10.1016/0014-5793(85)80374-4] [PMID: 2411595] 
[14] 
Parker, J.M.; Guo, D.; Hodges, R.S. 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,  1986, 25(19), 5425-5432.
[http://dx.doi.org/10.1021/bi00367a013] [PMID: 2430611] 
[15] 
Thornton, J.M.; Edwards, M.S.; Taylor, W.R.; Barlow, D.J. Location of ‘continuous’ antigenic determinants in the protruding regions of proteins. EMBO J.,  1986, 5(2), 409-413.
[http://dx.doi.org/10.1002/j.1460-2075.1986.tb04226.x] [PMID: 2423325] 
[16] 
Jameson, B.A.; Wolf, H. The antigenic index: a novel algorithm for predicting antigenic determinants. Comput. Appl. Biosci.,  1988, 4(1), 181-186.
[PMID: 2454713] 
[17] 
Pellequer, J.L.; Westhof, E.; Van Regenmortel, M.H. Correlation between the location of antigenic sites and the prediction of turns in proteins. Immunol. Lett.,  1993, 36(1), 83-99.
[http://dx.doi.org/10.1016/0165-2478(93)90072-A] [PMID: 7688347] 
[18] 
Alix, A.J. Predictive estimation of protein linear epitopes by using the program PEOPLE. Vaccine,  1999, 18(3-4), 311-314.
[http://dx.doi.org/10.1016/S0264-410X(99)00329-1] [PMID: 10506656] 
[19] 
Odorico, M.; Pellequer, J.L. BEPITOPE: Predicting the location of continuous epitopes and patterns in proteins. J. Mol. Recognit.,  2003, 16(1), 20-22.
[http://dx.doi.org/10.1002/jmr.602] [PMID: 12557235] 
[20] 
Saha, S.; Raghava, G.P.S. BcePred:prediction B-cell epitopes in antigenic sequences using physico-chemical properties. In: Artificial Immune Systems,  2004, 197-204.
[21] 
Chang, H.T.; Liu, C.H.; Pai, T.W. Estimation and extraction of B-cell linear epitopes predicted by mathematical morphology approaches. J. Mol. Recognit.,  2008, 21(6), 431-441.
[http://dx.doi.org/10.1002/jmr.910] [PMID: 18680207] 
[22] 
Biqing li L-LZ, Le-Le Hu, Kai-Yan Feng, Guo-Hua Huang and Lei Chen Prediction of Linear B-Cell Epitopes with mRMR feature selection and analysis. Curr. Bioinform.,  2015, 11(999), 1-1.
[23] 
Blythe, M.J.; Flower, D.R. Benchmarking B cell epitope prediction: Underperformance of existing methods. Protein Sci.,  2005, 14(1), 246-248.
[http://dx.doi.org/10.1110/ps.041059505] [PMID: 15576553] 
[24] 
Greenbaum, J.A.; Andersen, P.H.; Blythe, M.; Bui, H.H.; Cachau, R.E.; Crowe, J.; Davies, M.; Kolaskar, A.S.; Lund, O.; Morrison, S.; Mumey, B.; Ofran, Y.; Pellequer, J.L.; Pinilla, C.; Ponomarenko, J.V.; Raghava, G.P.; van Regenmortel, M.H.; Roggen, E.L.; Sette, A.; Schlessinger, A.; Sollner, J.; Zand, M.; Peters, B. Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools. J. Mol. Recognit.,  2007, 20(2), 75-82.
[http://dx.doi.org/10.1002/jmr.815] [PMID: 17205610] 
[25] 
Saha, S.; Raghava, G.P. Prediction of continuous B-cell epitopes in an antigen using recurrent neural network. Proteins,  2006, 65(1), 40-48.
[http://dx.doi.org/10.1002/prot.21078] [PMID: 16894596] 
[26] 
Larsen, J.E.; Lund, O.; Nielsen, M. Improved method for predicting linear B-cell epitopes. Immunome Res.,  2006, 2, 2.
[http://dx.doi.org/10.1186/1745-7580-2-2] [PMID: 16635264] 
[27] 
Chen, J.; Liu, H.; Yang, J.; Chou, K.C. Prediction of linear B-cell epitopes using amino acid pair antigenicity scale. Amino Acids,  2007, 33(3), 423-428.
[http://dx.doi.org/10.1007/s00726-006-0485-9] [PMID: 17252308] 
[28] 
El-Manzalawy, Y.; Dobbs, D.; Honavar, V. Predicting linear B-cell epitopes using string kernels. J. Mol. Recognit.,  2008, 21(4), 243-255.
[http://dx.doi.org/10.1002/jmr.893] [PMID: 18496882] 
[29] 
El-Manzalawy, Y.; Dobbs, D.; Honavar, V. Predicting flexible length linear B-cell epitopes. Comput. Syst. Bioinformatics Conf.,  2008, 7, 121-132.
[http://dx.doi.org/10.1142/9781848162648_0011] [PMID: 19642274] 
[30] 
Sollner, J.; Grohmann, R.; Rapberger, R.; Perco, P.; Lukas, A.; Mayer, B. Analysis and prediction of protective continuous B-cell epitopes on pathogen proteins. Immunome Res.,  2008, 4, 1.
[http://dx.doi.org/10.1186/1745-7580-4-1] [PMID: 18179690] 
[31] 
Sweredoski, M.J.; Baldi, P. COBEpro: A novel system for predicting continuous B-cell epitopes. Protein Eng. Des. Sel.,  2009, 22(3), 113-120.
[http://dx.doi.org/10.1093/protein/gzn075] [PMID: 19074155] 
[32] 
Guedes, R.L.M.; Rodrigues, C.M.F.; Coatnoan, N.; Cosson, A.; Cadioli, F.A.; Garcia, H.A.; Gerber, A.L.; Machado, R.Z.; Minoprio, P.M.C.; Teixeira, M.M.G.; de Vasconcelos, A.T.R. A comparative
in silico linear B-cell epitope prediction and characterization
for South American and African Trypanosoma vivax strains. Genomics,,  2018, S0888-7543(18)30126-5.
[PMID: 29499243] 
[33] 
Wee, L.J.; Simarmata, D.; Kam, Y.W.; Ng, L.F.; Tong, J.C. SVM-based prediction of linear B-cell epitopes using bayes feature extraction. BMC Genomics,  2010, 11(Suppl. 4), S21.
[http://dx.doi.org/10.1186/1471-2164-11-S4-S21] [PMID: 21143805] 
[34] 
Wang, H.W.; Lin, Y.C.; Pai, T.W.; Chang, H.T. Prediction of B-cell linear epitopes with a combination of support vector machine classification and amino acid propensity identification. J. Biomed. Biotechnol.,  2011, 2011, 432830.
[http://dx.doi.org/ 10.1155/2011/432830] [PMID: 21876642] 
[35] 
Wang, Y.; Wu, W.; Negre, N.N.; White, K.P.; Li, C.; Shah, P.K. Determinants of antigenicity and specificity in immune response for protein sequences. BMC Bioinformatics,  2011, 12, 251.
[http://dx.doi.org/10.1186/1471-2105-12-251] [PMID: 21693021] 
[36] 
Yao, B.; Zhang, L.; Liang, S.; Zhang, C. SVMTriP: a method to predict antigenic epitopes using support vector machine to integrate tri-peptide similarity and propensity. PLoS One,  2012, 7(9), e45152.
[http://dx.doi.org/10.1371/journal.pone.0045152] [PMID: 22984622] 
[37] 
Singh, H.; Ansari, H.R.; Raghava, G.P. Improved method for linear B-cell epitope prediction using antigen’s primary sequence. PLoS One,  2013, 8(5), e62216.
[http://dx.doi.org/10.1371/journal.pone.0062216] [PMID: 23667458] 
[38] 
Lian, Y.; Ge, M.; Pan, X.M. EPMLR: sequence-based linear B-cell epitope prediction method using multiple linear regression. BMC Bioinformatics,  2014, 15, 414.
[http://dx.doi.org/10.1186/s12859-014-0414-y] [PMID: 25523327] 
[39] 
Honavar YE-MaV. Building classifier ensembles for B-cell epitope prediction. Methods Mol. Biol.,  2014, 1184, 10.
[40] 
El-Manzalawy, Y.H.V. A framework for developing epitope prediction tools. Proceedings of the First ACM International conference on bioinformatics and computational biology,  2010, pp. 660-662.
[http://dx.doi.org/10.1145/1854776.1854906] 
[41] 
Saravanan, V.; Gautham, N. Harnessing computational biology for exact linear b-cell epitope prediction: A novel amino acid composition-based feature descriptor. OMICS,  2015, 19(10), 648-658.
[http://dx.doi.org/10.1089/omi.2015.0095] [PMID: 26406767] 
[42] 
Jespersen, M.C.; Peters, B.; Nielsen, M.; Marcatili, P. BepiPred-2.0: Improving sequence-based B-cell epitope prediction using conformational epitopes. Nucleic Acids Res.,  2017, 45(W1), W24-W29.
[http://dx.doi.org/10.1093/nar/gkx346] [PMID: 28472356] 
[43] 
Ansari, H.R.; Raghava, G.P. Identification of conformational B-cell epitopes in an antigen from its primary sequence. Immunome Res.,  2010, 6, 6.
[http://dx.doi.org/10.1186/1745-7580-6-6] [PMID: 20961417] 
[44] 
Gao, J.; Faraggi, E.; Zhou, Y.; Ruan, J.; Kurgan, L. BEST: Improved prediction of B-cell epitopes from antigen sequences. PLoS One,  2012, 7(6), e40104.
[http://dx.doi.org/10.1371/journal.pone.0040104] [PMID: 22761950] 
[45] 
Zhang, W.; Niu, Y.; Xiong, Y.; Zhao, M.; Yu, R.; Liu, J. Computational prediction of conformational B-cell epitopes from antigen primary structures by ensemble learning. PLoS One,  2012, 7(8), e43575.
[http://dx.doi.org/10.1371/journal.pone.0043575] [PMID: 22927994] 
[46] 
Zhang, J.; Zhao, X.; Sun, P.; Gao, B.; Ma, Z. Conformational B-cell epitopes prediction from sequences using cost-sensitive ensemble classifiers and spatial clustering. BioMed Res. Int.,  2014, 2014, 689219.
[PMID: 25045691] 
[47] 
Kulkarni-Kale, U; Bhosle, S; Kolaskar, AS A conformational
epitope prediction server. Nucleic Acids Res,  2005, 33(Web Server issue), W168- W 171.
[http://dx.doi.org/10.1093/nar/gki460] 
[48] 
Kolaskar, A.S.; Kulkarni-Kale, U. Prediction of three-dimensional structure and mapping of conformational epitopes of envelope glycoprotein of Japanese encephalitis virus. Virology,  1999, 261(1), 31-42.
[http://dx.doi.org/10.1006/viro.1999.9859] [PMID: 10441554] 
[49] 
Haste Andersen, P.; Nielsen, M.; Lund, O. Prediction of residues in discontinuous B-cell epitopes using protein 3D structures. Protein Sci.,  2006, 15(11), 2558-2567.
[http://dx.doi.org/10.1110/ps.062405906] [PMID: 17001032] 
[50] 
Sweredoski, M.J.; Baldi, P. PEPITO: Improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure. Bioinformatics,  2008, 24(12), 1459-1460.
[http://dx.doi.org/10.1093/bioinformatics/btn199] [PMID: 18443018] 
[51] 
Moreau, V.; Fleury, C.; Piquer, D.; Nguyen, C.; Novali, N.; Villard, S.; Laune, D.; Granier, C.; Molina, F. PEPOP: computational design of immunogenic peptides. BMC Bioinformatics,  2008, 9, 71.
[http://dx.doi.org/10.1186/1471-2105-9-71] [PMID: 18234071] 
[52] 
Qi, T; Qiu, T; Zhang, Q; Tang, K; Fan, Y; Qiu, J; Wu, D; Zhang, W; Chen, Y; Gao, J SEPPA 2.0-more refined server to predict spatial
epitope considering species of immune host and subcellular localiza-
tion of protein antigen. Nucleic. Acids Res,  2014, 42(Web
Server issue), W59-63.
[53] 
Sun, J.; Wu, D.; Xu, T.; Wang, X.; Xu, X.; Tao, L.; Li, Y.X.; Cao, Z.W. A computational server for spatial epitope prediction
of protein antigens. Nucleic Acids Res,  2009, 37(Web Server issue), W612-616.
[http://dx.doi.org/10.1093/nar/gkp417] 
[54] 
Rubinstein, N.D.; Mayrose, I.; Martz, E.; Pupko, T. Epitopia: a web-server for predicting B-cell epitopes. BMC Bioinformatics,  2009, 10, 287.
[http://dx.doi.org/10.1186/1471-2105-10-287] [PMID: 19751513] 
[55] 
Liang, S.; Zheng, D.; Zhang, C.; Zacharias, M. Prediction of antigenic epitopes on protein surfaces by consensus scoring. BMC Bioinformatics,  2009, 10, 302.
[http://dx.doi.org/10.1186/1471-2105-10-302] [PMID: 19772615] 
[56] 
Liang, S.; Zheng, D.; Standley, D.M.; Yao, B.; Zacharias, M.; Zhang, C. EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results. BMC Bioinformatics,  2010, 11, 381.
[http://dx.doi.org/10.1186/1471-2105-11-381] [PMID: 20637083] 
[57] 
Zhang, W.; Xiong, Y.; Zhao, M.; Zou, H.; Ye, X.; Liu, J. Prediction of conformational B-cell epitopes from 3D structures by random forests with a distance-based feature. BMC Bioinformatics,  2011, 12, 341.
[http://dx.doi.org/10.1186/1471-2105-12-341] [PMID: 21846404] 
[58] 
Zhao, L.; Hoi, S.C.; Li, Z.; Wong, L.; Nguyen, H.; Li, J. Coupling graphs, efficient algorithms and b-cell epitope prediction. IEEE/ACM Trans. Comput. Biol. Bioinformatics,  2014, 11(1), 7-16.
[http://dx.doi.org/10.1109/TCBB.2013.136] [PMID: 26355502] 
[59] 
Hu, Y.J.; Lin, S.C.; Lin, Y.L.; Lin, K.H.; You, S.N. A meta-learning approach for B-cell conformational epitope prediction. BMC Bioinformatics,  2014, 15, 378.
[http://dx.doi.org/10.1186/s12859-014-0378-y] [PMID: 25403375] 
[60] 
Yao, B.; Zheng, D.; Liang, S.; Zhang, C. Conformational B-cell epitope prediction on antigen protein structures: A review of current algorithms and comparison with common binding site prediction methods. PLoS One,  2013, 8(4), e62249.
[http://dx.doi.org/ 10.1371/journal.pone.0062249] [PMID: 23620816] 
[61] 
Geysen, H.M.; Rodda, S.J.; Mason, T.J. A priori delineation of a peptide which mimics a discontinuous antigenic determinant. Mol. Immunol.,  1986, 23(7), 709-715.
[http://dx.doi.org/10.1016/0161-5890(86)90081-7] [PMID: 2432410] 
[62] 
Moreau, V.; Granier, C.; Villard, S.; Laune, D.; Molina, F. Discontinuous epitope prediction based on mimotope analysis. Bioinformatics,  2006, 22(9), 1088-1095.
[http://dx.doi.org/10.1093/bioinformatics/btl012] [PMID: 16434442] 
[63] 
Mumey, B.; Angel, N.O.T. Filtering epitope alignments to improve
protein surface prediction. ISPA., 2006.In: ISPA; Springer, 2006,
pp. 648-657. 
[http://dx.doi.org/10.1007/11942634_67] 
[64] 
Mumey, B.M.; Bailey, B.W.; Kirkpatrick, B.; Jesaitis, A.J.; Angel, T.; Dratz, E.A. A new method for mapping discontinuous antibody epitopes to reveal structural features of proteins. J. Comput. Biol.,  2003, 10(3-4), 555-567.
[http://dx.doi.org/10.1089/10665270360688183] [PMID: 12935344] 
[65] 
Enshell-Seijffers, D.; Denisov, D.; Groisman, B.; Smelyanski, L.; Meyuhas, R.; Gross, G.; Denisova, G.; Gershoni, J.M. The mapping and reconstitution of a conformational discontinuous B-cell epitope of HIV-1. J. Mol. Biol.,  2003, 334(1), 87-101.
[http://dx.doi.org/10.1016/j.jmb.2003.09.002] [PMID: 14596802] 
[66] 
Bublil, E.M.; Freund, N.T.; Mayrose, I.; Penn, O.; Roitburd-Berman, A.; Rubinstein, N.D.; Pupko, T.; Gershoni, J.M. Stepwise prediction of conformational discontinuous B-cell epitopes using the Mapitope algorithm. Proteins,  2007, 68(1), 294-304.
[http://dx.doi.org/10.1002/prot.21387] [PMID: 17427229] 
[67] 
Halperin, I.; Wolfson, H.; Nussinov, R. SiteLight: binding-site prediction using phage display libraries. Protein Sci.,  2003, 12(7), 1344-1359.
[http://dx.doi.org/10.1110/ps.0237103] [PMID: 12824481] 
[68] 
Schreiber, A.; Humbert, M.; Benz, A.; Dietrich, U. 3D-Epitope-Explorer (3DEX): localization of conformational epitopes within three-dimensional structures of proteins. J. Comput. Chem.,  2005, 26(9), 879-887.
[http://dx.doi.org/10.1002/jcc.20229] [PMID: 15834923] 
[69] 
Mayrose, I.; Shlomi, T.; Rubinstein, N.D.; Gershoni, J.M.; Ruppin, E.; Sharan, R.; Pupko, T. Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm. Nucleic Acids Res.,  2007, 35(1), 69-78.
[http://dx.doi.org/10.1093/nar/gkl975] [PMID: 17151070] 
[70] 
Huang, J.; Gutteridge, A.; Honda, W.; Kanehisa, M. MIMOX: a web tool for phage display based epitope mapping. BMC Bioinformatics,  2006, 7, 451.
[http://dx.doi.org/10.1186/1471-2105-7-451] [PMID: 17038191] 
[71] 
Castrignanò, T.; De Meo, P.D.; Carrabino, D.; Orsini, M.; Floris, M.; Tramontano, A. The MEPS server for identifying protein conformational epitopes. BMC Bioinformatics,  2007, 8(Suppl. 1), S6.
[http://dx.doi.org/10.1186/1471-2105-8-S1-S6] [PMID: 17430573] 
[72] 
Mayrose, I.; Penn, O.; Erez, E.; Rubinstein, N.D.; Shlomi, T.; Freund, N.T.; Bublil, E.M.; Ruppin, E.; Sharan, R.; Gershoni, J.M.; Martz, E.; Pupko, T. Pepitope: Epitope mapping from affinity-selected peptides. Bioinformatics,  2007, 23(23), 3244-3246.
[http://dx.doi.org/10.1093/bioinformatics/btm493] [PMID: 17977889] 
[73] 
Negi, S.S.; Braun, W. Automated detection of conformational epitopes using phage display Peptide sequences. Bioinform. Biol. Insights,  2009, 3, 71-81.
[http://dx.doi.org/10.4137/BBI.S2745] [PMID: 20140073] 
[74] 
Huang, Y.X.; Bao, Y.L.; Guo, S.Y.; Wang, Y.; Zhou, C.G.; Li, Y.X. Pep-3D-Search: a method for B-cell epitope prediction based on mimotope analysis. BMC Bioinformatics,  2008, 9, 538.
[http://dx.doi.org/10.1186/1471-2105-9-538] [PMID: 19087303] 
[75] 
Chen, W.H.; Sun, P.P.; Lu, Y.; Guo, W.W.; Huang, Y.X.; Ma, Z.Q. MimoPro: A more efficient Web-based tool for epitope prediction using phage display libraries. BMC Bioinformatics,  2011, 12, 199.
[http://dx.doi.org/10.1186/1471-2105-12-199] [PMID: 21609501] 
[76] 
Chen, W.; Guo, W.W.; Huang, Y.; Ma, Z. PepMapper: A collaborative web tool for mapping epitopes from affinity-selected peptides. PLoS One,  2012, 7(5), e37869.
[http://dx.doi.org/10.1371/journal.pone.0037869] [PMID: 22701536] 
[77] 
Sun, P.; Ju, H.; Zhang, B.; Gu, Y.; Liu, B.; Huang, Y.; Zhang, H.; Li, Y. Conformational B-cell epitope prediction method based on antigen preprocessing and mimotopes analysis. BioMed Res. Int.,  2015, 2015, 257030.
[PMID: 25705652] 
[78] 
Sun, P.; Qi, J.; Zhao, Y.; Huang, Y.; Yang, G.; Ma, Z.; Li, Y. A novel conformational B-cell epitope prediction method based on mimotope and patch analysis. J. Theor. Biol.,  2016, 394, 102-108.
[http://dx.doi.org/10.1016/j.jtbi.2016.01.021] [PMID: 26804644] 
[79] 
Sun, P.; Chen, W.; Huang, Y.; Wang, H.; Ma, Z.; Lv, Y. Epitope prediction based on random peptide library screening: benchmark dataset and prediction tools evaluation. Molecules,  2011, 16(6), 4971-4993.
[http://dx.doi.org/10.3390/molecules16064971] [PMID: 21681149] 
[80] 
Zhang, C.; Li, Y.; Tang, W.; Zhou, Z.; Sun, P.; Ma, Z. The Relationship between B-cell epitope and mimotope sequences. Protein Pept. Lett.,  2016, 23(2), 132-141.
[http://dx.doi.org/10.2174/0929866523666151230124538] [PMID: 26715528] 
[81] 
Rapberger, R.; Lukas, A.; Mayer, B. Identification of discontinuous antigenic determinants on proteins based on shape complementarities. J. Mol. Recognit.,  2007, 20(2), 113-121.
[http://dx.doi.org/10.1002/jmr.819] [PMID: 17421048] 
[82] 
Soga, S.; Kuroda, D.; Shirai, H.; Kobori, M.; Hirayama, N. Use of amino acid composition to predict epitope residues of individual antibodies. Protein Eng. Des. Sel.,  2010, 23(6), 441-448.
[http://dx.doi.org/10.1093/protein/gzq014] [PMID: 20304974] 
[83] 
Krawczyk, K.; Liu, X.; Baker, T.; Shi, J.; Deane, C.M. Improving B-cell epitope prediction and its application to global antibody-antigen docking. Bioinformatics,  2014, 30(16), 2288-2294.
[http://dx.doi.org/10.1093/bioinformatics/btu190] [PMID: 24753488] 
[84] 
Ma, C.Z.B.S.W.T.P.S.Z. Prediction of conformational B-cell epitope binding with individual antibodies using phage display peptides. Int. J. Clin. Exp. Med.,  2016, 9(2), 10.
[85] 
Yiqi, L. Min, X.; Li, L.; Yu, H.; Ge, S.; Zhang, J.; Xia, N. Using a machine-learning approach to predict discontinuous antibody-specific b-cell epitopes. Curr. Bioinform.,  2017, 9(12), 5.
[86] 
Ashkenazy, H; Erez, E; Martz, E; Pupko, T ConSurf
2010: Calculating evolutionary conservation in sequence and structure
of proteins and nucleic acids. Nucleic Acids Res,  2010, 38(Web Server issue), W529-W533.
[87] 
Neuvirth, H.; Raz, R.; Schreiber, G. ProMate: A structure based prediction program to identify the location of protein-protein binding sites. J. Mol. Biol.,  2004, 338(1), 181-199.
[http://dx.doi.org/10.1016/j.jmb.2004.02.040] [PMID: 15050833] 
[88] 
Liang, S.; Zhang, C.; Liu, S.; Zhou, Y. Protein binding site prediction using an empirical scoring function. Nucleic Acids Res.,  2006, 34(13), 3698-3707.
[http://dx.doi.org/10.1093/nar/gkl454] [PMID: 16893954] 
[89] 
Kufareva, I.; Budagyan, L.; Raush, E.; Totrov, M.; Abagyan, R. PIER: Protein interface recognition for structural proteomics. Proteins,  2007, 67(2), 400-417.
[http://dx.doi.org/10.1002/prot.21233] [PMID: 17299750] 
Cite As
Current Topics in Medicinal Chemistry

Advances in In-silico B-cell Epitope Prediction

Abstract

Graphical Abstract
