Antigen-antibody interface properties: composition, residue interactions, and features of 53 non-redundant structures.

[1]  R. Poljak,et al.  Three-dimensional structure of an antigen–antibody complex at 6 Å resolution , 1985, Nature.

[2]  R. Poljak,et al.  Three-dimensional structure of an antigen-antibody complex at 2.8 A resolution , 1986, Science.

[3]  J. Thornton,et al.  Continuous and discontinuous protein antigenic determinants , 1986, Nature.

[4]  J. Rodgers,et al.  Thirteen ways to look at the correlation coefficient , 1988 .

[5]  S J Rodda,et al.  Cognitive features of continuous antigenic determinants , 1988, Journal of molecular recognition : JMR.

[6]  A. Lesk,et al.  Conformations of immunoglobulin hypervariable regions , 1989, Nature.

[7]  J. Scott,et al.  Searching for peptide ligands with an epitope library. , 1990, Science.

[8]  P Argos,et al.  Evolution of protein cores. Constraints in point mutations as observed in globin tertiary structures. , 1990, Journal of molecular biology.

[9]  G. Air,et al.  Epitopes on protein antigens: Misconceptions and realities , 1990, Cell.

[10]  T. N. Bhat,et al.  Small rearrangements in structures of Fv and Fab fragments of antibody D 1.3 on antigen binding , 1990, Nature.

[11]  I. Mian,et al.  Structure, function and properties of antibody binding sites. , 1991, Journal of molecular biology.

[12]  R. Houghten,et al.  Functional importance of amino acid residues making up peptide antigenic determinants. , 1993, Molecular immunology.

[13]  Algirdas J. Jesaitis,et al.  Topological Mapping of Neutrophil Cytochrome b Epitopes with Phage-display Libraries (*) , 1995, The Journal of Biological Chemistry.

[14]  M. Sanner,et al.  Reduced surface: an efficient way to compute molecular surfaces. , 1996, Biopolymers.

[15]  G. Cohen,et al.  Interactions of protein antigens with antibodies. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[16]  A. Jesaitis,et al.  Filamentous phage display of oligopeptide libraries. , 1996, Analytical biochemistry.

[17]  S. Jones,et al.  Principles of protein-protein interactions. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[18]  Andrew J. Martin,et al.  Antibody-antigen interactions: contact analysis and binding site topography. , 1996, Journal of molecular biology.

[19]  M. V. Regenmortel,et al.  Mapping Epitope Structure and Activity: From One-Dimensional Prediction to Four-Dimensional Description of Antigenic Specificity , 1996 .

[20]  P Argos,et al.  Applying experimental data to protein fold prediction with the genetic algorithm. , 1997, Protein engineering.

[21]  D. Baker,et al.  Prediction of local structure in proteins using a library of sequence-structure motifs. , 1998, Journal of molecular biology.

[22]  Algirdas J. Jesaitis,et al.  Antibody Imprint of a Membrane Protein Surface , 1998, The Journal of Biological Chemistry.

[23]  A. Bogan,et al.  Anatomy of hot spots in protein interfaces. , 1998, Journal of molecular biology.

[24]  C. Chothia,et al.  The atomic structure of protein-protein recognition sites. , 1999, Journal of molecular biology.

[25]  E A Dratz,et al.  Actin surface structure revealed by antibody imprints: Evaluation of phage‐display analysis of anti‐actin antibodies , 2008, Protein science : a publication of the Protein Society.

[26]  K. Bennett,et al.  Probing protein surface topology by chemical surface labeling, crosslinking, and mass spectrometry. , 2000, Methods in molecular biology.

[27]  R. Meloen,et al.  Mimotopes: realization of an unlikely concept , 2000, Journal of molecular recognition : JMR.

[28]  S. Smith‐Gill,et al.  Three-dimensional structures of the free and antigen-bound Fab from monoclonal antilysozyme antibody HyHEL-63(,). , 2000, Biochemistry.

[29]  W. Delano Unraveling hot spots in binding interfaces: progress and challenges. , 2002, Current opinion in structural biology.

[30]  R. Mariuzza,et al.  Molecular recognition in antibody-antigen complexes. , 2002, Advances in protein chemistry.

[31]  Christopher Bystroff,et al.  Fully automated ab initio protein structure prediction using I-STES, HMMSTR and ROSETTA , 2002, ISMB.

[32]  Brendan J. McConkey,et al.  Quantification of protein surfaces, volumes and atom-atom contacts using a constrained Voronoi procedure , 2002, Bioinform..

[33]  Bonnie Kirkpatrick,et al.  A New Method for Mapping Discontinuous Antibody Epitopes to Reveal Structural Features of Proteins , 2003, J. Comput. Biol..

[34]  Brendan Mumey,et al.  Constraints on the conformation of the cytoplasmic face of dark‐adapted and light‐excited rhodopsin inferred from antirhodopsin antibody imprints , 2003, Protein science : a publication of the Protein Society.

[35]  Bonnie Kirkpatrick,et al.  Mapping discontinuous antibody epitopes to reveal protein structure and changes in structure related to function , 2003, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003.

[36]  B. McConkey,et al.  Discrimination of native protein structures using atom–atom contact scoring , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[37]  Jonathan M Gershoni,et al.  The mapping and reconstitution of a conformational discontinuous B-cell epitope of HIV-1. , 2003, Journal of molecular biology.

[38]  Ruth Nussinov,et al.  SiteLight: Binding‐site prediction using phage display libraries , 2003, Protein science : a publication of the Protein Society.

[39]  Christopher Bystroff,et al.  Ab Initio Protein Structure Prediction Using Pathway Models , 2003, Comparative and functional genomics.

[40]  R. Nussinov,et al.  Protein–protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[41]  Frederic A. Fellouse,et al.  Phage-displayed antibody libraries of synthetic heavy chain complementarity determining regions. , 2004, Journal of molecular biology.

[42]  Sachdev S Sidhu,et al.  Synthetic antibodies from a four-amino-acid code: a dominant role for tyrosine in antigen recognition. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[43]  A. Jesaitis,et al.  Site-Specific Inhibitors of NADPH Oxidase Activity and Structural Probes of Flavocytochrome b: Characterization of Six Monoclonal Antibodies to the p22phox Subunit1 , 2004, The Journal of Immunology.

[44]  ANDREAS SCHREIBER,et al.  3D‐Epitope‐Explorer (3DEX): Localization of conformational epitopes within three‐dimensional structures of proteins , 2005, J. Comput. Chem..

[45]  Brendan Mumey,et al.  Filtering Epitope Alignments to Improve Protein Surface Prediction , 2006, ISPA Workshops.

[46]  Malin M. Young,et al.  Structure and dynamics of dark‐state bovine rhodopsin revealed by chemical cross‐linking and high‐resolution mass spectrometry , 2006, Protein science : a publication of the Protein Society.

[47]  Violaine Moreau,et al.  Discontinuous epitope prediction based on mimotope analysis , 2006, Bioinform..

[48]  Minoru Kanehisa,et al.  MIMOX: a web tool for phage display based epitope mapping , 2006, BMC Bioinformatics.

[49]  Avner Schlessinger,et al.  Towards a consensus on datasets and evaluation metrics for developing B‐cell epitope prediction tools , 2007, Journal of molecular recognition : JMR.

[50]  R. Bahadur,et al.  The interface of protein-protein complexes: Analysis of contacts and prediction of interactions , 2008, Cellular and Molecular Life Sciences.

[51]  M. V. Regenmortel Antigenicity and Immunogenicity of Viral Proteins , 2008 .

[52]  Yuxin Li,et al.  Pep-3D-Search: a method for B-cell epitope prediction based on mimotope analysis , 2008, BMC Bioinformatics.

[53]  Sachdev S Sidhu,et al.  The intrinsic contributions of tyrosine, serine, glycine and arginine to the affinity and specificity of antibodies. , 2008, Journal of molecular biology.

[54]  Young Jin Lee Mass spectrometric analysis of cross-linking sites for the structure of proteins and protein complexes. , 2008 .

[55]  M. V. Van Regenmortel,et al.  Structure-activity relationships in peptide-antibody complexes: implications for epitope prediction and development of synthetic peptide vaccines. , 2009, Current medicinal chemistry.

[56]  Susan Jones,et al.  ProtorP: a protein-protein interaction analysis server , 2009, Bioinform..

[57]  M. V. Regenmortel,et al.  What is a B-cell epitope? , 2009 .

[58]  Laura M. Palermo,et al.  Structural Comparison of Different Antibodies Interacting with Parvovirus Capsids , 2009, Journal of Virology.

[59]  Mark R. Chance,et al.  Structural waters define a functional channel mediating activation of the GPCR, rhodopsin , 2009, Proceedings of the National Academy of Sciences.

[60]  Shohei Koide,et al.  The importance of being tyrosine: lessons in molecular recognition from minimalist synthetic binding proteins. , 2009, ACS chemical biology.

[61]  R. Nussinov,et al.  The role of dynamic conformational ensembles in biomolecular recognition. , 2009, Nature chemical biology.

[62]  Yang Lu,et al.  MimoPro: a more efficient Web-based tool for epitope prediction using phage display libraries , 2011, BMC Bioinformatics.

[63]  Jamie K. Scott,et al.  Exploring peptide mimics for the production of antibodies against discontinuous protein epitopes. , 2010, Molecular immunology.