Computational characterization of B-cell epitopes

Allcorn, 2002, SACS—self-maintaining database of antibody crystal structure information, Bioinformatics, 18, 175, 10.1093/bioinformatics/18.1.175

Aloy, 2001, Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking, J. Mol. Biol., 311, 395, 10.1006/jmbi.2001.4870

Arnon, 1969, Antibodies to a unique region in lysozyme provoked by a synthetic antigen conjugate, Proc. Natl. Acad. Sci. U.S.A., 62, 163, 10.1073/pnas.62.1.163

Atassi, 1975, Antigenic structure of myoglobin: the complete immunochemical anatomy of a protein and conclusions relating to antigenic structures of proteins, Immunochemistry, 12, 423, 10.1016/0019-2791(75)90010-5

Atassi, 1978, Precise determination of the entire antigenic structure of lysozyme: molecular features of protein antigenic structures and potential of “surface-simulation” synthesis—a powerful new concept for protein binding sites, Immunochemistry, 15, 909, 10.1016/0161-5890(78)90126-8

Baker, 2001, Electrostatics of nanosystems: application to microtubules and the ribosome, Proc. Natl. Acad. Sci. U.S.A., 98, 10037, 10.1073/pnas.181342398

Benjamin, 1984, The antigenic structure of proteins: a reappraisal, Annu. Rev. Immunol., 2, 67, 10.1146/annurev.iy.02.040184.000435

Benjamini, 1995, Controlling the false discovery rate: a practical and powerful approach to multiple testing, J. Roy. Stat. Soc., 57, 289

Berman, 2000, The protein data bank, Nucl. Acids Res., 28, 235, 10.1093/nar/28.1.235

Berzofsky, 1985, Intrinsic and extrinsic factors in protein antigenic structure, Science, 229, 932, 10.1126/science.2410982

Boeckmann, 2003, The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003, Nucl. Acids Res., 31, 365, 10.1093/nar/gkg095

Bogan, 1998, Anatomy of hot spots in protein interfaces, J. Mol. Biol., 280, 1, 10.1006/jmbi.1998.1843

Bublil, 2007, Stepwise prediction of conformational discontinuous B-cell epitopes using the mapitope algorithm, Proteins: Struct. Funct. Genet., 68, 294, 10.1002/prot.21387

Chakrabarti, 2002, Dissecting protein–protein recognition sites, Proteins: Struct. Funct. Genet., 47, 334, 10.1002/prot.10085

Enshell-Seijffers, 2003, The mapping and reconstitution of a conformational discontinuous B-cell epitope of HIV-1, J. Mol. Biol., 334, 87, 10.1016/j.jmb.2003.09.002

Hopp, 1986, Protein surface analysis. Methods for identifying antigenic determinants and other interaction sites, J. Immunol. Methods, 88, 1, 10.1016/0022-1759(86)90045-1

Hopp, 1981, Prediction of protein antigenic determinants from amino acid sequences, Proc. Natl. Acad. Sci. U.S.A., 78, 3824, 10.1073/pnas.78.6.3824

Irving, 2001, Random-peptide libraries and antigen-fragment libraries for epitope mapping and the development of vaccines and diagnostics, Curr. Opin. Chem. Biol., 5, 314, 10.1016/S1367-5931(00)00208-8

Jackson, 1999, Comparison of protein–protein interactions is serine protease-inhibitor and antibody–antigen complexes: implications for the protein docking problem, Protein Sci., 8, 603, 10.1110/ps.8.3.603

Jemmerson, 1979, Topographic antigenic determinants on cytochrome c. Immunoadsorbent separation of the rabbit antibody populations directed against horse cytochrome, J. Biol. Chem., 254, 12706, 10.1016/S0021-9258(19)86371-8

Jemmerson, 1985, Mobility and evolutionary variability factors in protein antigenicity, Nature, 317, 89, 10.1038/317089b0

Jerne, 1960, Immunological speculations, Annu. Rev. Microbiol., 14, 341, 10.1146/annurev.mi.14.100160.002013

Jones, 1995, Protein–protein interactions: a review of protein dimer structures, Prog. Biophys. Mol. Biol., 63, 31, 10.1016/0079-6107(94)00008-W

Jones, 1996, Principles of protein–protein interactions, Proc. Natl. Acad. Sci. U.S.A., 93, 13, 10.1073/pnas.93.1.13

Jones, 1997, Analysis of protein–protein interaction sites using surface patches, J. Mol. Biol., 272, 121, 10.1006/jmbi.1997.1234

Jones, 1997, Prediction of protein–protein interaction sites using patch analysis, J. Mol. Biol., 272, 133, 10.1006/jmbi.1997.1233

Kabsch, 1983, Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features, Biopolymers, 22, 2577, 10.1002/bip.360221211

Landgraf, 2001, Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins, J. Mol. Biol., 307, 1487, 10.1006/jmbi.2001.4540

Laver, 1990, Epitopes on protein antigens: misconceptions and realities, Cell, 61, 553, 10.1016/0092-8674(90)90464-P

Lilienfeld, 1994

Lo Conte, 1999, The atomic structure of protein–protein recognition sites, J. Mol. Biol., 285, 2177, 10.1006/jmbi.1998.2439

Ma, 2003, Protein–protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces, Proc. Natl. Acad. Sci. U.S.A., 100, 5772, 10.1073/pnas.1030237100

Mayrose, 2004, Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior, Mol. Biol. Evol., 21, 1781, 10.1093/molbev/msh194

Miller, 1987, Interior and surface of monomeric proteins, J. Mol. Biol., 196, 641, 10.1016/0022-2836(87)90038-6

Murzin, 1995, SCOP: a structural classification of proteins database for the investigation of sequences and structures, J. Mol. Biol., 247, 536, 10.1016/S0022-2836(05)80134-2

Neuvirth, 2004, ProMate: a structure based prediction program to identify the location of protein–protein binding sites, J. Mol. Biol., 338, 181, 10.1016/j.jmb.2004.02.040

Nimrod, 2005, In silico identification of functional regions in proteins, Bioinformatics, 21, i328, 10.1093/bioinformatics/bti1023

Novotny, 1986, Antigenic determinants in proteins coincide with surface regions accessible to large probes (antibody domains), Proc. Natl. Acad. Sci. U.S.A., 83, 226, 10.1073/pnas.83.2.226

Pellequer, 1991, Predicting location of continuous epitopes in proteins from their primary structures, Methods Enzymol., 203, 176, 10.1016/0076-6879(91)03010-E

Saunders, 2002, Evaluation of structural and evolutionary contributions to deleterious mutation prediction, J. Mol. Biol., 322, 891, 10.1016/S0022-2836(02)00813-6

Shindyalov, 1998, Protein structure alignment by incremental combinatorial extension (CE) of the optimal path, Protein Eng., 11, 739, 10.1093/protein/11.9.739

Shoemaker, 2007, Deciphering protein–protein interactions. Part I. Experimental techniques and databases, PLoS Comput. Biol., 3

Simpson, 1951, The interpretation of interaction in contingency tables, J. Roy. Stat. Soc., 13, 238

Sobolev, 1999, Automated analysis of interatomic contacts in proteins, Bioinformatics, 15, 327, 10.1093/bioinformatics/15.4.327

Sokal, 1995

Thornton, 1986, Location of ‘continuous’ antigenic determinants in the protruding regions of proteins, EMBO J., 5, 409, 10.1002/j.1460-2075.1986.tb04226.x

Tsodikov, 2002, Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature, J. Comput. Chem., 23, 600, 10.1002/jcc.10061

Valdar, 2001, Conservation helps to identify biologically relevant crystal contacts, J. Mol. Biol., 313, 399, 10.1006/jmbi.2001.5034

Westhof, 1984, Correlation between segmental mobility and the location of antigenic determinants in proteins, Nature, 311, 123, 10.1038/311123a0

Westwood, 2001

Zhou, 2001, Prediction of protein interaction sites from sequence profile and residue neighbor list, Proteins: Struct. Funct. Genet., 44, 336, 10.1002/prot.1099