Identification of protein-protein interaction sites from docking energy landscapes.

[1]  Zhiping Weng,et al.  A protein–protein docking benchmark , 2003, Proteins.

[2]  R. Abagyan,et al.  ICM‐DISCO docking by global energy optimization with fully flexible side‐chains , 2003, Proteins.

[3]  M. Reibarkh,et al.  Interatomic potentials and solvation parameters from protein engineering data for buried residues , 2002, Protein science : a publication of the Protein Society.

[4]  Barry Honig,et al.  On the role of electrostatic interactions in the design of protein-protein interfaces. , 2002, Journal of molecular biology.

[5]  R. Abagyan,et al.  Soft protein–protein docking in internal coordinates , 2002, Protein science : a publication of the Protein Society.

[6]  Sandor Vajda,et al.  Protein-protein association kinetics and protein docking. , 2002, Current Opinion in Structural Biology.

[7]  M. Sternberg,et al.  Prediction of protein-protein interactions by docking methods. , 2002, Current opinion in structural biology.

[8]  Ruben Abagyan,et al.  Screened Charge Electrostatic Model in Protein-Protein Docking Simulations , 2002, Pacific Symposium on Biocomputing.

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

[10]  D. Eisenberg,et al.  Protein interaction databases. , 2001, Current opinion in biotechnology.

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

[12]  R C Wade,et al.  Protein-protein association: investigation of factors influencing association rates by brownian dynamics simulations. , 2001, Journal of molecular biology.

[13]  A. Elcock,et al.  Computer Simulation of Protein−Protein Interactions , 2001 .

[14]  Robert B. Raffa,et al.  DRUG-RECEPTOR THERMODYNAMICS : introduction and applications , 2001 .

[15]  G. Kachalova,et al.  A redox‐dependent interaction between two electron‐transfer partners involved in photosynthesis , 2000, EMBO reports.

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

[17]  H. Wolfson,et al.  Examination of shape complementarity in docking of Unbound proteins , 1999, Proteins.

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

[19]  I. Vakser,et al.  A systematic study of low-resolution recognition in protein--protein complexes. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

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

[21]  G. Tollin,et al.  Electrostatic forces involved in orienting Anabaena ferredoxin during binding to Anabaena ferredoxin:NAdp+ reductase: Site‐specific mutagenesis, transient kinetic measurements, and electrostatic surface potentials , 1999, Protein science : a publication of the Protein Society.

[22]  Robert M. Stroud,et al.  Efficiency of signalling through cytokine receptors depends critically on receptor orientation , 1998, Nature.

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

[24]  Lode Wyns,et al.  Potent enzyme inhibitors derived from dromedary heavy‐chain antibodies , 1998, The EMBO journal.

[25]  T. Clackson,et al.  Structural and functional analysis of the 1:1 growth hormone:receptor complex reveals the molecular basis for receptor affinity. , 1998, Journal of molecular biology.

[26]  M J Sternberg,et al.  Predictive docking of protein-protein and protein-DNA complexes. , 1998, Current opinion in structural biology.

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

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

[29]  J. Janin The kinetics of protein‐protein recognition , 1997, Proteins.

[30]  Biologie Structurales The Kinetics of Protein-Protein Recognition , 1997 .

[31]  Ruben Abagyan,et al.  Protein structure prediction by global energy optimization , 1997 .

[32]  R Abagyan,et al.  Flexible protein–ligand docking by global energy optimization in internal coordinates , 1997, Proteins.

[33]  Pedro M. Alzari,et al.  A potent new mode of β-lactamase inhibition revealed by the 1.7 Å X-ray crystallographic structure of the TEM-1–BLIP complex , 1996, Nature Structural Biology.

[34]  T. Arakawa,et al.  Dimerization of the extracellular domain of the erythropoietin (EPO) receptor by EPO: one high-affinity and one low-affinity interaction. , 1996, Biochemistry.

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

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

[37]  J M Thornton,et al.  Protein-protein interactions: a review of protein dimer structures. , 1995, Progress in biophysics and molecular biology.

[38]  S Vajda,et al.  Effect of conformational flexibility and solvation on receptor-ligand binding free energies. , 1994, Biochemistry.

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

[40]  Ruben Abagyan,et al.  ICM—A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation , 1994, J. Comput. Chem..

[41]  Structural and kinetic characterization of a beta-lactamase-inhibitor protein. , 1994, Nature.

[42]  C. Betzel,et al.  Molecular structure of the acyl-enzyme intermediate in β-lactam hydrolysis at 1.7 Å resolution , 1992, Nature.

[43]  P Argos,et al.  Optimal protocol and trajectory visualization for conformational searches of peptides and proteins. , 1992, Journal of molecular biology.

[44]  D. Eisenberg,et al.  Atomic solvation parameters applied to molecular dynamics of proteins in solution , 1992, Protein science : a publication of the Protein Society.

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

[46]  R. Bruccoleri,et al.  On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3, and HyHEL-5. , 1989, Biochemistry.

[47]  C Chothia,et al.  Surface, subunit interfaces and interior of oligomeric proteins. , 1988, Journal of molecular biology.

[48]  R W Pickersgill,et al.  A rapid method of calculating charge-charge interaction energies in proteins. , 1988, Protein engineering.

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

[50]  Ralph G. Pearson,et al.  Ionization potentials and electron affinities in aqueous solution , 1986 .

[51]  A. D. McLachlan,et al.  Solvation energy in protein folding and binding , 1986, Nature.

[52]  P. Goodford A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. , 1985, Journal of medicinal chemistry.

[53]  H. Kamin,et al.  Electron transfer by ferredoxin:NADP+ reductase. Rapid-reaction evidence for participation of a ternary complex. , 1984, The Journal of biological chemistry.

[54]  P M Cullis,et al.  Affinities of amino acid side chains for solvent water. , 1981, Biochemistry.

[55]  J. Janin,et al.  Computer analysis of protein-protein interaction. , 1978, Journal of molecular biology.

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

[57]  John A. Nelder,et al.  A Simplex Method for Function Minimization , 1965, Comput. J..

[58]  N. Metropolis,et al.  Equation of State Calculations by Fast Computing Machines , 1953, Resonance.