Protein--protein recognition: juxtaposition of domain and interface cores in immunoglobulins and other sandwich-like proteins.

[1]  C. Levinthal Are there pathways for protein folding , 1968 .

[2]  C. Chothia,et al.  Principles of protein–protein recognition , 1975, Nature.

[3]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1978, Archives of biochemistry and biophysics.

[4]  M. V. Volkenstein,et al.  Electronic-conformational interactions in biopolymers , 1979 .

[5]  C. Chothia,et al.  Relative orientation of close-packed beta-pleated sheets in proteins. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[6]  M Karplus,et al.  Dynamics of proteins: elements and function. , 1983, Annual review of biochemistry.

[7]  M. L. Connolly Solvent-accessible surfaces of proteins and nucleic acids. , 1983, Science.

[8]  C. Chothia,et al.  Domain association in immunoglobulin molecules. The packing of variable domains. , 1985, Journal of molecular biology.

[9]  P. Argos An investigation of protein subunit and domain interfaces. , 1988, Protein engineering.

[10]  S. Miller The structure of interfaces between subunits of dimeric and tetrameric proteins. , 1989, Protein engineering.

[11]  Ina Ruck,et al.  USA , 1969, The Lancet.

[12]  S. Miller Protein-protein recognition and the association of immunoglobulin constant domains. , 1990, Journal of molecular biology.

[13]  R L Stanfield,et al.  Major antigen-induced domain rearrangements in an antibody. , 1993, Structure.

[14]  I M Gelfand,et al.  Analysis of the relation between the sequence and secondary and three-dimensional structures of immunoglobulin molecules. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[15]  M. Gerstein,et al.  Average core structures and variability measures for protein families: application to the immunoglobulins. , 1995, Journal of molecular biology.

[16]  A G Murzin,et al.  SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.

[17]  G Schreiber,et al.  Energetics of protein-protein interactions: analysis of the barnase-barstar interface by single mutations and double mutant cycles. , 1995, Journal of molecular biology.

[18]  I M Gelfand,et al.  The invariant system of coordinates of antibody molecules: prediction of the "standard" C alpha framework of VL and VH domains. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[19]  F. Cohen,et al.  An evolutionary trace method defines binding surfaces common to protein families. , 1996, Journal of molecular biology.

[20]  G. Vriend,et al.  Molecular docking using surface complementarity , 1996, Proteins.

[21]  S. Jones,et al.  Analysis of protein-protein interaction sites using surface patches. , 1997, Journal of molecular biology.

[22]  S. Jones,et al.  Prediction of protein-protein interaction sites using patch analysis. , 1997, Journal of molecular biology.

[23]  A. Fersht Nucleation mechanisms in protein folding. , 1997, Current opinion in structural biology.

[24]  Chris Sander,et al.  The HSSP database of protein structure-sequence alignments and family profiles , 1998, Nucleic Acids Res..

[25]  A J Olson,et al.  Morphology of protein-protein interfaces. , 1998, Structure.

[26]  I. Gelfand,et al.  Geometric invariant core for the V(L) and V(H) domains of immunoglobulin molecules. , 1998, Protein engineering.

[27]  C Chothia,et al.  Structural determinants in the sequences of immunoglobulin variable domain. , 1998, Journal of molecular biology.

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

[29]  J. Thornton,et al.  PQS: a protein quaternary structure file server. , 1998, Trends in biochemical sciences.

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

[31]  G. Rose,et al.  Is protein folding hierarchic? I. Local structure and peptide folding. , 1999, Trends in biochemical sciences.

[32]  Jaime Prilusky,et al.  Automated analysis of interatomic contacts in proteins , 1999, Bioinform..

[33]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[34]  Rafael Najmanovich,et al.  Side‐chain flexibility in proteins upon ligand binding , 2000, Proteins.

[35]  R. Norel,et al.  Electrostatic aspects of protein-protein interactions. , 2000, Current opinion in structural biology.

[36]  Casimir A. Kulikowski,et al.  Geometric Invariant Core for the CL and CH1 Domains of Immunoglobulin Molecules , 2000, J. Comput. Biol..

[37]  F. Cohen,et al.  Co-evolution of proteins with their interaction partners. , 2000, Journal of molecular biology.

[38]  M. Sternberg,et al.  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. , 2001, Journal of molecular biology.

[39]  Gideon Schreiber,et al.  New insights into the mechanism of protein–protein association , 2001, Proteins.

[40]  L. Mirny,et al.  Evolutionary conservation of the folding nucleus. , 2000, Journal of molecular biology.

[41]  D. Eisenberg,et al.  Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins. , 2001, Journal of molecular biology.

[42]  J. Thornton,et al.  Protein–protein interfaces: Analysis of amino acid conservation in homodimers , 2001, Proteins.

[43]  N. Ben-Tal,et al.  Residue frequencies and pairing preferences at protein–protein interfaces , 2001, Proteins.

[44]  Huan‐Xiang Zhou,et al.  Prediction of protein interaction sites from sequence profile and residue neighbor list , 2001, Proteins.

[45]  Igor N Berezovsky,et al.  Loop Fold Structure of Proteins: Resolution of Levinthal's Paradox , 2002, Journal of biomolecular structure & dynamics.

[46]  N. Kannan,et al.  Analysis of homodimeric protein interfaces by graph-spectral methods. , 2002, Protein engineering.

[47]  D. Baker,et al.  A simple physical model for binding energy hot spots in protein–protein complexes , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[48]  Sabine Dietmann,et al.  Prediction of 3D neighbours of molecular surface patches in proteins by artificial neural networks , 2002, Bioinform..

[49]  O. Lichtarge,et al.  Structural clusters of evolutionary trace residues are statistically significant and common in proteins. , 2002, Journal of molecular biology.

[50]  O. Lichtarge,et al.  Evolutionary predictions of binding surfaces and interactions. , 2002, Current opinion in structural biology.

[51]  Ariel Fernández,et al.  Insufficiently dehydrated hydrogen bonds as determinants of protein interactions , 2002, Proceedings of the National Academy of Sciences of the United States of America.

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

[53]  A. Valencia,et al.  Prediction of protein--protein interaction sites in heterocomplexes with neural networks. , 2002, European journal of biochemistry.

[54]  A. Finkelstein Cunning Simplicity of a Hierarchical Folding , 2002, Journal of biomolecular structure & dynamics.

[55]  Israel M. Gelfand,et al.  Common features in structures and sequences of sandwich-like proteins , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[56]  J. Janin,et al.  Dissecting protein–protein recognition sites , 2002, Proteins.

[57]  Patrick Aloy,et al.  Interrogating protein interaction networks through structural biology , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[58]  M. Desmadril,et al.  Key interactions in neocarzinostatin, a protein of the immunoglobulin fold family. , 2002, Protein engineering.

[59]  Christian Cole,et al.  Side‐chain conformational entropy at protein–protein interfaces , 2002, Protein science : a publication of the Protein Society.

[60]  B. Rost,et al.  Analysing six types of protein-protein interfaces. , 2003, Journal of molecular biology.

[61]  H. Scheraga,et al.  Amino Acid Residues at Protein−Protein Interfaces: Why Is Propensity so Different from Relative Abundance? , 2003 .

[62]  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.

[63]  R. Jimenez,et al.  Protein dynamics and the immunological evolution of molecular recognition. , 2004, Proceedings of the National Academy of Sciences of the United States of America.