메뉴 건너뛰기




Volumn 5, Issue 1, 2012, Pages 11-21

B-Pred, a structure based B-cell epitopes prediction server

Author keywords

B cell epitopes; Bioinformatics; Epitope prediction; Immunoinformatics; Web server

Indexed keywords


EID: 84878890474     PISSN: None     EISSN: 11786949     Source Type: Journal    
DOI: 10.2147/AABC.S30620     Document Type: Article
Times cited : (17)

References (35)
  • 1
    • 0024381924 scopus 로고
    • Structural and functional approaches to the study of protein antigenicity
    • Van Regenmortel MH. Structural and functional approaches to the study of protein antigenicity. Immunol Today. 1989;10(8):266-272.
    • (1989) Immunol Today. , vol.10 , Issue.8 , pp. 266-272
    • Van Regenmortel, M.H.1
  • 2
    • 78149293634 scopus 로고    scopus 로고
    • Recent advances in B-cell epitope prediction methods
    • El-Manzalawy Y, Honavar V. Recent advances in B-cell epitope prediction methods. Immunome Res. 2010;6(Suppl 2):S2.
    • (2010) Immunome Res. , vol.6 , pp. S2
    • El-Manzalawy, Y.1    Honavar, V.2
  • 3
    • 64049090391 scopus 로고    scopus 로고
    • An introduction to epitope prediction methods and software
    • Yang X, Yu X. An introduction to epitope prediction methods and software. Rev Med Virol. 2009;19(2):77-96.
    • (2009) Rev Med Virol. , vol.19 , Issue.2 , pp. 77-96
    • Yang, X.1    Yu, X.2
  • 4
    • 0000448982 scopus 로고
    • Prediction of protein antigenic determinants from amino acid sequences
    • Hopp TP, Woods KR. Prediction of protein antigenic determinants from amino acid sequences. Proc Nat Acad Sci U S A. 1981;78(6): 3824-3828.
    • (1981) Proc Nat Acad Sci U S A. , vol.78 , Issue.6 , pp. 3824-3828
    • Hopp, T.P.1    Woods, K.R.2
  • 6
    • 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. 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.
    • (1986) Biochemistry. , vol.25 , Issue.19 , pp. 5425-5432
    • Parker, J.M.1    Guo, D.2    Hodges, R.S.3
  • 7
    • 0025605617 scopus 로고
    • A semi-empirical method for prediction of antigenic determinants on protein antigens
    • Kolaskar AS, Tongaonkar PC. A semi-empirical method for prediction of antigenic determinants on protein antigens. FEBS Lett. 1990;276(1-2): 172-174.
    • (1990) FEBS Lett. , vol.276 , Issue.1-2 , pp. 172-174
    • Kolaskar, A.S.1    Tongaonkar, P.C.2
  • 8
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • Kyte J, Doolittle RF. A simple method for displaying the hydropathic character of a protein. J Mol Biol. 1982;157(1):105-132.
    • (1982) J Mol Biol. , vol.157 , Issue.1 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2
  • 9
    • 0027156564 scopus 로고
    • Correlation between the location of antigenic sites and the prediction of turns in proteins
    • Pellequer JL, Westhof E, Vanregenmortel MHV. Correlation between the location of antigenic sites and the prediction of turns in proteins. Immunol Lett. 1993;36(1):83-100.
    • (1993) Immunol Lett. , vol.36 , Issue.1 , pp. 83-100
    • Pellequer, J.L.1    Westhof, E.2    Vanregenmortel, M.H.V.3
  • 10
    • 11144246404 scopus 로고    scopus 로고
    • Benchmarking B cell epitope prediction: underperformance of existing methods
    • Blythe MJ, Flower DR. Benchmarking B cell epitope prediction: underperformance of existing methods. Protein Sci. 2005;14(1): 246-248.
    • (2005) Protein Sci. , vol.14 , Issue.1 , pp. 246-248
    • Blythe, M.J.1    Flower, D.R.2
  • 11
    • 56749156105 scopus 로고    scopus 로고
    • Estimation and extraction of B-cell linear epitopes predicted by mathematical morphology approaches
    • Chang HT, Liu CH, Pai TW. Estimation and extraction of B-cell linear epitopes predicted by mathematical morphology approaches. J Mol Recognit. 2008;21(6):431-441.
    • (2008) J Mol Recognit. , vol.21 , Issue.6 , pp. 431-441
    • Chang, H.T.1    Liu, C.H.2    Pai, T.W.3
  • 12
    • 79959282758 scopus 로고    scopus 로고
    • Determinants of antigenicity and specificity in immune response for protein sequences
    • Wang Y, Wu W, Negre NN, White KP, Li C, Shah PK. Determinants of antigenicity and specificity in immune response for protein sequences. BMC Bioinformatics. 2011;12:251.
    • (2011) BMC Bioinformatics. , vol.12 , pp. 251
    • Wang, Y.1    Wu, W.2    Negre, N.N.3    White, K.P.4    Li, C.5    Shah, P.K.6
  • 13
    • 37749042370 scopus 로고    scopus 로고
    • Antibody-protein interactions: benchmark datasets and prediction tools evaluation
    • Ponomarenko JV, Bourne PE. Antibody-protein interactions: benchmark datasets and prediction tools evaluation. BMC Struct Biol. 2007; 7:64.
    • (2007) BMC Struct Biol. , vol.7 , pp. 64
    • Ponomarenko, J.V.1    Bourne, P.E.2
  • 14
    • 77957984965 scopus 로고    scopus 로고
    • Identification of conformational B-cell Epitopes in an antigen from its primary sequence
    • Ansari HR, Raghava GP. Identification of conformational B-cell Epitopes in an antigen from its primary sequence. Immunome Res. 2010;6:6.
    • (2010) Immunome Res. , vol.6 , pp. 6
    • Ansari, H.R.1    Raghava, G.P.2
  • 15
    • 78650628653 scopus 로고    scopus 로고
    • A generic approach to evaluate how B-cell epitopes are surface-exposed on protein structures
    • Lollier V, Denery-Papini S, Larré C, Tessier D. A generic approach to evaluate how B-cell epitopes are surface-exposed on protein structures. Mol Immunol. 2011;48(4):577-585.
    • (2011) Mol Immunol. , vol.48 , Issue.4 , pp. 577-585
    • Lollier, V.1    Denery-Papini, S.2    Larré, C.3    Tessier, D.4
  • 16
    • 58049187138 scopus 로고    scopus 로고
    • ElliPro: a new structure-based tool for the prediction of antibody epitopes
    • Ponomarenko J, Bui HH, Li W, et al. ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics. 2008;9:514.
    • (2008) BMC Bioinformatics. , vol.9 , pp. 514
    • Ponomarenko, J.1    Bui, H.H.2    Li, W.3
  • 17
    • 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, Liu J. Prediction of conformational B-cell epitopes from 3D structures by random forests with a distance-based feature. BMC Bioinformatics. 2011;12:341.
    • (2011) BMC Bioinformatics. , vol.12 , pp. 341
    • Zhang, W.1    Xiong, Y.2    Zhao, M.3    Zou, H.4    Ye, X.5    Liu, J.6
  • 18
    • 75549084463 scopus 로고    scopus 로고
    • The immune epitope database 2.0
    • Vita R, Zarebski L, Greenbaum JA, et al. The immune epitope database 2.0. Nucleic Acids Res. 2010;38(Database issue):D854-D862.
    • (2010) Nucleic Acids Res. , vol.38 , Issue.DATABASE ISSUE , pp. D854-D862
    • Vita, R.1    Zarebski, L.2    Greenbaum, J.A.3
  • 20
    • 0025830469 scopus 로고
    • A method to identify protein sequences that fold into a known three-dimensional structure
    • Bowie JU, Lüthy R, Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science. 1991;253(5016):164-170.
    • (1991) Science. , vol.253 , Issue.5016 , pp. 164-170
    • Bowie, J.U.1    Lüthy, R.2    Eisenberg, D.3
  • 21
    • 0026610767 scopus 로고
    • Assessment of protein models with three-dimensional profiles
    • Lüthy R, Bowie JU, Eisenberg D. Assessment of protein models with three-dimensional profiles. Nature. 1992;356(6364):83-85.
    • (1992) Nature. , vol.356 , Issue.6364 , pp. 83-85
    • Lüthy, R.1    Bowie, J.U.2    Eisenberg, D.3
  • 22
    • 0030767485 scopus 로고    scopus 로고
    • VERIFY3D: assessment of protein models with three-dimensional profiles
    • Eisenberg D, Lüthy R, Bowie JU. VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol. 1997;277: 396-404.
    • (1997) Methods Enzymol. , vol.277 , pp. 396-404
    • Eisenberg, D.1    Lüthy, R.2    Bowie, J.U.3
  • 23
    • 16344373015 scopus 로고    scopus 로고
    • Protein homology detection by HMM-HMM comparison
    • Söding J. Protein homology detection by HMM-HMM comparison. Bioinformatics. 2005;21(7):951-960.
    • (2005) Bioinformatics. , vol.21 , Issue.7 , pp. 951-960
    • Söding, J.1
  • 24
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol. 1993;234(3):779-815.
    • (1993) J Mol Biol. , vol.234 , Issue.3 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 25
    • 48849113878 scopus 로고    scopus 로고
    • Comparative protein structure modeling using MODELLER
    • Chapter 2: Unit 2.9
    • Eswar N, Webb B, Marti-Renom MA, et al. Comparative protein structure modeling using MODELLER. Curr Protoc Protein Sci. 2007;Chapter 2:Unit 2.9.
    • (2007) Curr Protoc Protein Sci.
    • Eswar, N.1    Webb, B.2    Marti-Renom, M.A.3
  • 26
    • 0015222647 scopus 로고
    • The interpretation of protein structures: estimation of static accessibility
    • Lee B, Richards FM. The interpretation of protein structures: estimation of static accessibility. J Mol Biol. 1971;55(3):379-400.
    • (1971) J Mol Biol. , vol.55 , Issue.3 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 27
    • 85044818423 scopus 로고    scopus 로고
    • Version 2.1.1. Manchester, UK: Hubbard S, Thornton JM. Accessed March 14, 2011.
    • Naccess [computer program]. Version 2.1.1. Manchester, UK: Hubbard S, Thornton JM; 1996. Available from: http://www.bioinf.manchester.ac.uk/naccess/. Accessed March 14, 2011.
    • (1996)
  • 28
    • 85044822647 scopus 로고    scopus 로고
    • Jmol: an open-source Java viewer for chemical structures in 3D [computer program]
    • Version 11.8.24. Minnesota, MN: Jmol Development Team. Accessed April 12, 2011.
    • Jmol: an open-source Java viewer for chemical structures in 3D [computer program]. Version 11.8.24. Minnesota, MN: Jmol Development Team; 2010. Available from: http://jmol.sourceforge.net/. Accessed April 12, 2011.
    • (2010)
  • 29
    • 85044816528 scopus 로고    scopus 로고
    • JpGraph [computer program]
    • Version 3.0.7. Japan: Asial Corporation. Accessed April 12, 2011.
    • JpGraph [computer program]. Version 3.0.7. Japan: Asial Corporation; 2011. Available from: http://jpgraph.net/. Accessed April 12, 2011.
    • (2011)
  • 31
    • 67650215667 scopus 로고    scopus 로고
    • Prediction of linear B-cell epitopes
    • Reimer U. Prediction of linear B-cell epitopes. Methods Mol Biol. 2009; 524:335-344.
    • (2009) Methods Mol Biol. , vol.524 , pp. 335-344
    • Reimer, U.1
  • 32
    • 79952436419 scopus 로고    scopus 로고
    • Structural biology: breaking the protein rules
    • Chouard T. Structural biology: breaking the protein rules. Nature. 2011; 471(7337):151-153.
    • (2011) Nature. , vol.471 , Issue.7337 , pp. 151-153
    • Chouard, T.1
  • 33
    • 77949916296 scopus 로고    scopus 로고
    • Understanding protein non-folding
    • Uversky VN, Dunker AK. Understanding protein non-folding. Biochim Biophys Acta. 2010;1804(6):1231-1264.
    • (2010) Biochim Biophys Acta. , vol.1804 , Issue.6 , pp. 1231-1264
    • Uversky, V.N.1    Dunker, A.K.2
  • 34
    • 84856710192 scopus 로고    scopus 로고
    • Identification of amino acid propensities that are strong determinants of linear B-cell epitope using neural networks
    • Su CH, Pal NR, Lin KL, Chung IF. Identification of amino acid propensities that are strong determinants of linear B-cell epitope using neural networks. PLoS One. 2012;7(2):e30617.
    • (2012) PLoS One. , vol.7 , Issue.2
    • Su, C.H.1    Pal, N.R.2    Lin, K.L.3    Chung, I.F.4
  • 35
    • 39549095936 scopus 로고    scopus 로고
    • Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines
    • Bui HH, Sidney J, Li W, Fusseder N, Sette A. Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines. BMC Bioinformatics. 2007;8:361.
    • (2007) BMC Bioinformatics. , vol.8 , pp. 361
    • Bui, H.H.1    Sidney, J.2    Li, W.3    Fusseder, N.4    Sette, A.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.