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Antibody-protein interactions: benchmark datasets and prediction tools evaluation.

Ponomarenko JV, Bourne PE.

BMC Struct Biol. 2007 Oct 2;7:64.PMID: 17910770 [PubMed - indexed for MEDLINE]Related articlesFree article

ElliPro: a new structure-based tool for the prediction of antibody epitopes.

Ponomarenko J, Bui HH, Li W, Fusseder N, Bourne PE, Sette A, Peters B.

BMC Bioinformatics. 2008 Dec 2;9:514.PMID: 19055730 [PubMed - indexed for MEDLINE]Related articlesFree article

Prediction of residues in discontinuous B-cell epitopes using protein 3D structures.

Haste Andersen P, Nielsen M, Lund O.

Protein Sci. 2006 Nov;15(11):2558-67. Epub 2006 Sep 25.PMID: 17001032 [PubMed - indexed for MEDLINE]Related articlesFree article

Pep-3D-Search: a method for B-cell epitope prediction based on mimotope analysis.

Huang YX, Bao YL, Guo SY, Wang Y, Zhou CG, Li YX.

BMC Bioinformatics. 2008 Dec 16;9:538.PMID: 19087303 [PubMed - indexed for MEDLINE]Related articlesFree article

Evaluation of MHC-II peptide binding prediction servers: applications for vaccine research.

Lin HH, Zhang GL, Tongchusak S, Reinherz EL, Brusic V.

BMC Bioinformatics. 2008 Dec 12;9 Suppl 12:S22.PMID: 19091022 [PubMed - indexed for MEDLINE]Related articlesFree article

Automated identification of complementarity determining regions (CDRs) reveals peculiar characteristics of CDRs and B cell epitopes.

Ofran Y, Schlessinger A, Rost B.

J Immunol. 2008 Nov 1;181(9):6230-5.PMID: 18941213 [PubMed - indexed for MEDLINE]Related articlesFree article

Computational characterization of B-cell epitopes.

Rubinstein ND, Mayrose I, Halperin D, Yekutieli D, Gershoni JM, Pupko T.

Mol Immunol. 2008 Jul;45(12):3477-89. Epub 2007 Nov 26.PMID: 18023478 [PubMed - indexed for MEDLINE]Related articles

On evaluating MHC-II binding peptide prediction methods.

El-Manzalawy Y, Dobbs D, Honavar V.

PLoS One. 2008 Sep 24;3(9):e3268.PMID: 18813344 [PubMed - indexed for MEDLINE]Related articlesFree article

Predicting B cell epitope residues with network topology based amino acid indices.

Huang J, Honda W, Kanehisa M.

Genome Inform. 2007;19:40-9.PMID: 18546503 [PubMed - indexed for MEDLINE]Related articlesFree article

Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction.

Larsen MV, Lundegaard C, Lamberth K, Buus S, Lund O, Nielsen M.

BMC Bioinformatics. 2007 Oct 31;8:424.PMID: 17973982 [PubMed - indexed for MEDLINE]Related articlesFree article

Predicting linear B-cell epitopes using string kernels.

El-Manzalawy Y, Dobbs D, Honavar V.

J Mol Recognit. 2008 Jul-Aug;21(4):243-55.PMID: 18496882 [PubMed - indexed for MEDLINE]Related articlesFree article

Characterization of antibody-binding sites on proteins: development of a knowledgebase and its applications in improving epitope prediction.

Ghate AD, Bhagwat BU, Bhosle SG, Gadepalli SM, Kulkarni-Kale UD.

Protein Pept Lett. 2007;14(6):531-5.PMID: 17627592 [PubMed - indexed for MEDLINE]Related articles

Pan-specific MHC class I predictors: a benchmark of HLA class I pan-specific prediction methods.

Zhang H, Lundegaard C, Nielsen M.

Bioinformatics. 2009 Jan 1;25(1):83-9. Epub 2008 Nov 7.PMID: 18996943 [PubMed - indexed for MEDLINE]Related articlesFree article

Prediction of linear B-cell epitopes.

Reimer U.

Methods Mol Biol. 2009;524:335-44.PMID: 19377956 [PubMed - indexed for MEDLINE]Related articles

Identification of discontinuous antigenic determinants on proteins based on shape complementarities.

Rapberger R, Lukas A, Mayer B.

J Mol Recognit. 2007 Mar-Apr;20(2):113-21.PMID: 17421048 [PubMed - indexed for MEDLINE]Related articles

A machine-learning approach for predicting B-cell epitopes.

Rubinstein ND, Mayrose I, Pupko T.

Mol Immunol. 2009 Feb;46(5):840-7. Epub 2008 Oct 22.PMID: 18947876 [PubMed - indexed for MEDLINE]Related articles

Estimation and extraction of B-cell linear epitopes predicted by mathematical morphology approaches.

Chang HT, Liu CH, Pai TW.

J Mol Recognit. 2008 Nov-Dec;21(6):431-41.PMID: 18680207 [PubMed - indexed for MEDLINE]Related articles

Analysis and prediction of protective continuous B-cell epitopes on pathogen proteins.

Sollner J, Grohmann R, Rapberger R, Perco P, Lukas A, Mayer B.

Immunome Res. 2008 Jan 7;4:1.PMID: 18179690 [PubMed - in process]Related articlesFree article

Epitome: database of structure-inferred antigenic epitopes.

Schlessinger A, Ofran Y, Yachdav G, Rost B.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D777-80.PMID: 16381978 [PubMed - indexed for MEDLINE]Related articlesFree article

Structural evidence for recognition of a single epitope by two distinct antibodies.

Fleury D, Daniels RS, Skehel JJ, Knossow M, Bizebard T.

Proteins. 2000 Sep 1;40(4):572-8.PMID: 10899782 [PubMed - indexed for MEDLINE]Related articles