Predictive docking of protein-protein and protein-DNA complexes.

Recent developments in algorithms to predict the docking of two proteins have considered both the initial rigid-body global search and subsequent screening and refinement. The result of two blind trials of protein docking are encouraging--for complexes that are not too large and do not undergo sizeable conformational change upon association, the algorithms are now able to suggest reasonably accurate models.

[1]  J. Janin,et al.  Rigid‐body docking with mutant constraints of influenza hemagglutinin with antibody HC19 , 1994, Proteins.

[2]  R M Knegtel,et al.  MONTY: a Monte Carlo approach to protein-DNA recognition. , 1994, Journal of molecular biology.

[3]  D. Covell,et al.  Docking enzyme‐inhibitor complexes using a preference‐based free‐energy surface , 1996, Proteins.

[4]  R L Jernigan,et al.  A preference‐based free‐energy parameterization of enzyme‐inhibitor binding. Applications to HIV‐1‐protease inhibitor design , 1995, Protein science : a publication of the Protein Society.

[5]  D. Goodsell,et al.  Automated docking of substrates to proteins by simulated annealing , 1990, Proteins.

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

[7]  F E Cohen,et al.  Modeling protein-ligand complexes. , 1996, Current opinion in structural biology.

[8]  J. S. Dixon,et al.  Evaluation of the CASP2 docking section , 1997, Proteins.

[9]  H. Wolfson,et al.  Molecular surface complementarity at protein-protein interfaces: the critical role played by surface normals at well placed, sparse, points in docking. , 1995, Journal of molecular biology.

[10]  I A Vakser Long-distance potentials: an approach to the multiple-minima problem in ligand-receptor interaction. , 1996, Protein engineering.

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

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

[13]  G Cesareni,et al.  Escher: A new docking procedure applied to the reconstruction of protein tertiary structure , 1997, Proteins.

[14]  J. Janin,et al.  Protein docking algorithms: simulating molecular recognition , 1993 .

[15]  M J Sternberg,et al.  A continuum model for protein-protein interactions: application to the docking problem. , 1995, Journal of molecular biology.

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

[17]  J. Janin,et al.  Protein‐protein recognition analyzed by docking simulation , 1991, Proteins.

[18]  C. Aflalo,et al.  Hydrophobic docking: A proposed enhancement to molecular recognition techniques , 1994, Proteins.

[19]  M. Swindells,et al.  Protein clefts in molecular recognition and function. , 1996, Protein science : a publication of the Protein Society.

[20]  R M Knegtel,et al.  Monte Carlo docking of protein-DNA complexes: incorporation of DNA flexibility and experimental data. , 1994, Protein engineering.

[21]  I D Kuntz,et al.  Predicting the structure of protein complexes: a step in the right direction. , 1996, Chemistry & biology.

[22]  I. Vakser,et al.  Evaluation of GRAMM low‐resolution docking methodology on the hemagglutinin‐antibody complex , 1997, Proteins.

[23]  M. Lewis,et al.  Calculation of the free energy of association for protein complexes , 1992, Protein science : a publication of the Protein Society.

[24]  I. Vakser Protein docking for low-resolution structures. , 1995, Protein engineering.

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

[26]  R. Nussinov,et al.  A geometry-based suite of molecular docking processes. , 1995, Journal of molecular biology.

[27]  M. Sternberg,et al.  Modelling protein docking using shape complementarity, electrostatics and biochemical information. , 1997, Journal of molecular biology.

[28]  D E Koshland,et al.  Molecular recognition analyzed by docking simulations: the aspartate receptor and isocitrate dehydrogenase from Escherichia coli. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[29]  A. Olson,et al.  Shape analysis of molecular surfaces , 1993, Biopolymers.

[30]  A. Valencia,et al.  Correlated mutations contain information about protein-protein interaction. , 1997, Journal of molecular biology.

[31]  Randy J. Read,et al.  A multiple‐start Monte Carlo docking method , 1992 .

[32]  Ruben Abagyan,et al.  Detailed ab initio prediction of lysozyme–antibody complex with 1.6 Å accuracy , 1994, Nature Structural Biology.

[33]  M. Sternberg,et al.  Rapid refinement of protein interfaces incorporating solvation: application to the docking problem. , 1998, Journal of molecular biology.

[34]  E. Katchalski‐Katzir,et al.  Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[35]  D. Schomburg,et al.  Hydrogen bonding and molecular surface shape complementarity as a basis for protein docking. , 1996, Journal of molecular biology.

[36]  J. Janin,et al.  Protein-protein recognition. , 1995, Progress in biophysics and molecular biology.

[37]  I. Kuntz,et al.  Protein docking and complementarity. , 1991, Journal of molecular biology.

[38]  R. Read,et al.  Atomic solvation parameters in the analysis of protein‐protein docking results , 1995, Protein science : a publication of the Protein Society.

[39]  A. McCoy,et al.  Electrostatic complementarity at protein/protein interfaces. , 1997, Journal of molecular biology.

[40]  J. Cherfils,et al.  Molecular docking programs successfully predict the binding of a β-lactamase inhibitory protein to TEM-1 β-lactamase , 1996, Nature Structural Biology.

[41]  S Vajda,et al.  Prediction of protein complexes using empirical free energy functions , 1996, Protein science : a publication of the Protein Society.

[42]  Thomas Lengauer,et al.  Computational methods for biomolecular docking. , 1996, Current opinion in structural biology.

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