Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues.

[1]  Jie Liang,et al.  Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking. , 2004, Journal of molecular biology.

[2]  Ruth Nussinov,et al.  A method for simultaneous alignment of multiple protein structures , 2004, Proteins.

[3]  H. Wolfson,et al.  Protein-protein interactions; coupling of structurally conserved residues and of hot spots across interfaces. Implications for docking. , 2004, Structure.

[4]  H. Wolfson,et al.  A new, structurally nonredundant, diverse data set of protein–protein interfaces and its implications , 2004, Protein science : a publication of the Protein Society.

[5]  L. Mirny,et al.  Protein complexes and functional modules in molecular networks , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[6]  Sandor Vajda,et al.  CAPRI: A Critical Assessment of PRedicted Interactions , 2003, Proteins.

[7]  B. Rost,et al.  Predicted protein–protein interaction sites from local sequence information , 2003, FEBS letters.

[8]  Hui Lu,et al.  Multimeric threading-based prediction of protein-protein interactions on a genomic scale: application to the Saccharomyces cerevisiae proteome. , 2003, Genome research.

[9]  D. Eisenberg,et al.  Computational methods of analysis of protein-protein interactions. , 2003, Current opinion in structural biology.

[10]  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.

[11]  Hui Lu,et al.  Development of unified statistical potentials describing protein-protein interactions. , 2003, Biophysical journal.

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

[13]  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.

[14]  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.

[15]  L. Serrano,et al.  Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. , 2002, Journal of molecular biology.

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

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

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

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

[20]  H. Wolfson,et al.  Multiple diverse ligands binding at a single protein site : A matter of pre-existing populations , 2001 .

[21]  B Honig,et al.  Electrostatic contributions to protein–protein interactions: Fast energetic filters for docking and their physical basis , 2001, Protein science : a publication of the Protein Society.

[22]  K A Dill,et al.  Are proteins well-packed? , 2001, Biophysical journal.

[23]  Kurt S. Thorn,et al.  ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions , 2001, Bioinform..

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

[25]  A. Thomas,et al.  A fast method to predict protein interaction sites from sequences. , 2000, Journal of molecular biology.

[26]  A. Pommer,et al.  Specificity in protein-protein interactions: the structural basis for dual recognition in endonuclease colicin-immunity protein complexes. , 2000, Journal of molecular biology.

[27]  D. Eisenberg,et al.  Protein function in the post-genomic era , 2000, Nature.

[28]  R. Nussinov,et al.  Conservation of polar residues as hot spots at protein interfaces , 2000, Proteins.

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

[30]  W. Delano,et al.  Convergent solutions to binding at a protein-protein interface. , 2000, Science.

[31]  Colin Kleanthous,et al.  Protein-protein recognition , 2000 .

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

[33]  R M Jackson,et al.  Comparison of protein–protein interactions in serine protease‐inhibitor and antibody‐antigen complexes: Implications for the protein docking problem , 2008, Protein science : a publication of the Protein Society.

[34]  D. Eisenberg,et al.  Detecting protein function and protein-protein interactions from genome sequences. , 1999, Science.

[35]  B K Shoichet,et al.  Structure-based discovery and in-parallel optimization of novel competitive inhibitors of thymidylate synthase. , 1999, Chemistry & biology.

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

[37]  O. Ptitsyn,et al.  Empirical solvent‐mediated potentials hold for both intra‐molecular and inter‐molecular inter‐residue interactions , 1998, Protein science : a publication of the Protein Society.

[38]  I Bahar,et al.  Packing of sidechains in low-resolution models for proteins. , 1998, Folding & design.

[39]  R Nussinov,et al.  Protein folding via binding and vice versa. , 1998, Folding & design.

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

[41]  B. Matthews,et al.  The response of T4 lysozyme to large‐to‐small substitutions within the core and its relation to the hydrophobic effect , 1998, Protein science : a publication of the Protein Society.

[42]  R C Wade,et al.  Prediction of protein hydration sites from sequence by modular neural networks. , 1998, Protein engineering.

[43]  Joël Janin,et al.  Specific versus non-specific contacts in protein crystals , 1997, Nature Structural Biology.

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

[45]  H. Wolfson,et al.  A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique. , 1996, Journal of molecular biology.

[46]  R. Jernigan,et al.  Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. , 1996, Journal of molecular biology.

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

[48]  D. Ringe What makes a binding site a binding site? , 1995, Current opinion in structural biology.

[49]  T. Clackson,et al.  A hot spot of binding energy in a hormone-receptor interface , 1995, Science.

[50]  B K Shoichet,et al.  A relationship between protein stability and protein function. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[51]  J. Janin,et al.  Principles of protein-protein recognition from structure to thermodynamics. , 1995, Biochimie.

[52]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[53]  K A Dill,et al.  Side‐chain entropy and packing in proteins , 1994, Protein science : a publication of the Protein Society.

[54]  K. Dill,et al.  Modeling compact denatured states of proteins. , 1994, Biochemistry.

[55]  J. Thornton,et al.  Satisfying hydrogen bonding potential in proteins. , 1994, Journal of molecular biology.

[56]  D. Covell,et al.  A role for surface hydrophobicity in protein‐protein recognition , 1994, Protein science : a publication of the Protein Society.

[57]  S. Rackovsky,et al.  Prediction of protein conformation on the basis of a search for compact structures: Test on avian pancreatic polypeptide , 1993, Protein science : a publication of the Protein Society.

[58]  S. Henikoff,et al.  Amino acid substitution matrices from protein blocks. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[59]  C. Chothia One thousand families for the molecular biologist , 1992, Nature.

[60]  C. Chothia Proteins. One thousand families for the molecular biologist. , 1992, Nature.

[61]  H. Wolfson,et al.  Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[62]  B. Cunningham,et al.  Rational design of receptor-specific variants of human growth hormone. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[63]  R. M. Burnett,et al.  Distribution and complementarity of hydropathy in mutisunit proteins , 1991, Proteins.

[64]  C. Chothia,et al.  The structure of protein-protein recognition sites. , 1990, The Journal of biological chemistry.

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

[66]  Cyrus Chothia,et al.  The accessible surface area and stability of oligomeric proteins , 1987, Nature.

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

[68]  B. Lee,et al.  The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.