Structural analysis of B-cell epitopes in antibody:protein complexes
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Andersen, 2006, Prediction of residues in discontinuous B-cell epitopes using protein 3D structures, Protein Science, 15, 2558, 10.1110/ps.062405906
Bhat, 1994, Bound water molecules and conformational stabilization help mediate an antigen–antibody association, Proceedings of the National Academy of Sciences of the United States of America, 91, 1089, 10.1073/pnas.91.3.1089
Bickerton, 2011, Comprehensive, atomic-level characterization of structurally characterized protein–protein interactions: the PICCOLO database, BMC Bioinformatics, 12, 313, 10.1186/1471-2105-12-313
Bogan, 1998, Anatomy of hot spots in protein interfaces, Journal of Molecular Biology, 280, 1, 10.1006/jmbi.1998.1843
Bordner, 2005, Statistical analysis and prediction of protein–protein interfaces, Proteins, 60, 353, 10.1002/prot.20433
Chakrabarti, 2002, Dissecting protein–protein recognition sites, Proteins, 47, 334, 10.1002/prot.10085
Chen, 2007, Prediction of linear B-cell epitopes using amino acid pair antigenicity scale, Amino Acids, 33, 423, 10.1007/s00726-006-0485-9
Collis, 2003, Analysis of the antigen combining site: correlations between length and sequence composition of the hypervariable loops and the nature of the antigen, Journal of Molecular Biology, 325, 337, 10.1016/S0022-2836(02)01222-6
Lo Conte, 1999, The atomic structure of protein–protein recognition sites, Journal of Molecular Biology, 285, 2177, 10.1006/jmbi.1998.2439
Fellouse, 2005, Molecular recognition by a binary code, Journal of Molecular Biology, 348, 1153, 10.1016/j.jmb.2005.03.041
Gershoni, 2007, Epitope mapping: the first step in developing epitope-based vaccines, BioDrugs, 21, 145, 10.2165/00063030-200721030-00002
Hamelryck, 2005, An amino acid has two sides: a new 2D measure provides a different view of solvent exposure, Proteins, 59, 38, 10.1002/prot.20379
Hamelryck, 2003, PDB file parser and structure class implemented in Python, Bioinformatics, 19, 2308, 10.1093/bioinformatics/btg299
Hobohm, 1992, Selection of representative protein data sets, Protein Science, 1, 409, 10.1002/pro.5560010313
Huang, 2007, Predicting B cell epitope residues with network topology based amino acid indices, Genome Informatics, 19, 40
Igawa, 2011, Engineering the variable region of therapeutic IgG antibodies, Monoclonal Antibodies, 3, 243
Irving, 2001, Random-peptide libraries and antigen-fragment libraries for epitope mapping and the development of vaccines and diagnostics, Current Opinion in Chemical Biology, 5, 314, 10.1016/S1367-5931(00)00208-8
Kabsch, 1983, Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features, Biopolymers, 22, 2577, 10.1002/bip.360221211
Keskin, 2005, Hot regions in protein–protein interactions: the organization and contribution of structurally conserved hot spot residues, Journal of Molecular Biology, 345, 1281, 10.1016/j.jmb.2004.10.077
Knorr, 2000, Distance-based outliers: algorithms and applications, The VLDB Journal – The International Journal on Very Large Data Bases, 8, 237
Li, 2005, Magnitude of the hydrophobic effect at central versus peripheral sites in protein–protein interfaces, Structure, 13, 297, 10.1016/j.str.2004.12.012
Li, 2003, X-ray snapshots of the maturation of an antibody response to a protein antigen, Nature Structural & Molecular Biology, 10, 482, 10.1038/nsb930
Li, 2012, Progressive dry–core–wet–rim hydration trend in a nested-ring topology of protein binding interfaces, BMC Bioinformatics, 13, 51, 10.1186/1471-2105-13-51
Liang, 2010, EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results, BMC Bioinformatics, 11, 381, 10.1186/1471-2105-11-381
Lijnzaad, 1997, Hydrophobic patches on protein subunit interfaces: characteristics and prediction, Proteins, 28, 333, 10.1002/(SICI)1097-0134(199707)28:3<333::AID-PROT4>3.0.CO;2-D
Lollier, 2011, A generic approach to evaluate how B-cell epitopes are surface-exposed on protein structures, Molecular Immunology, 48, 577, 10.1016/j.molimm.2010.10.011
Lund, 2005
Ma, 2003, Protein–protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces, Proceedings of the National Academy of Sciences of the United States of America, 100, 5772, 10.1073/pnas.1030237100
MacCallum, 1996, Antibody–antigen interactions: contact analysis and binding site topography, Journal of Molecular Biology, 262, 732, 10.1006/jmbi.1996.0548
Martin, 2010, Protein sequence and structure analysis of antibody variable domains, 33
Neuvirth, 2004, ProMate: a structure based prediction program to identify the location of protein–protein binding sites, Journal of Molecular Biology, 338, 181, 10.1016/j.jmb.2004.02.040
Novotný, 1986, Antigenic determinants in proteins coincide with surface regions accessible to large probes (antibody domains), Proceedings of the National Academy of Sciences of the United States of America, 83, 226, 10.1073/pnas.83.2.226
Ofran, 2008, Automated identification of complementarity determining regions (CDRs) reveals peculiar characteristics of CDRs and B cell epitopes, Journal of Immunology, 181, 6230, 10.4049/jimmunol.181.9.6230
Ponomarenko, 2008, ElliPro: a new structure-based tool for the prediction of antibody epitopes, BMC Bioinformatics, 9, 514, 10.1186/1471-2105-9-514
Van Regenmortel, 2009, What is a B-cell epitope?, Methods in Molecular Biology, 524, 3, 10.1007/978-1-59745-450-6_1
Rubinstein, 2008, Computational characterization of B-cell epitopes, Molecular Immunology, 45, 3477, 10.1016/j.molimm.2007.10.016
Rubinstein, 2009, Epitopia: a web-server for predicting B-cell epitopes, BMC Bioinformatics, 10, 287, 10.1186/1471-2105-10-287
Shindyalov, 1998, Protein structure alignment by incremental combinatorial extension (CE) of the optimal path, Protein Engineering, 11, 739, 10.1093/protein/11.9.739
Sun, 2011, Does difference exist between epitope and non-epitope residues? Analysis of the physicochemical and structural properties on conformational epitopes from B-cell protein antigens, Immunome Research, 7, 1
Sundberg, 2003, Structural, energetic, and functional analysis of a protein–protein interface at distinct stages of affinity maturation, Structure, 11, 1151, 10.1016/S0969-2126(03)00187-4
Sweredoski, 2008, PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure, Bioinformatics, 24, 1459, 10.1093/bioinformatics/btn199
Sweredoski, 2009, COBEpro: a novel system for predicting continuous B-cell epitopes, Protein Engineering Design & Selection, 22, 113, 10.1093/protein/gzn075
Thornton, 1986, Location of “continuous” antigenic determinants in the protruding regions of proteins, EMBO Journal, 5, 409, 10.1002/j.1460-2075.1986.tb04226.x
Valdar, 2001, Conservation helps to identify biologically relevant crystal contacts, Journal of Molecular Biology, 313, 399, 10.1006/jmbi.2001.5034