"Soft docking": matching of molecular surface cubes.

[1]  J. Rebek Model studies in molecular recognition. , 1987, Science.

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

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

[4]  B Honig,et al.  Computer simulations of the diffusion of a substrate to an active site of an enzyme. , 1987, Science.

[5]  F R Salemme,et al.  An hypothetical structure for an intermolecular electron transfer complex of cytochromes c and b5. , 1976, Journal of molecular biology.

[6]  G. Roberts,et al.  Cooperativity in ligand binding to dihydrofolate reductase. , 1978, Biochemistry.

[7]  M. L. Connolly Shape complementarity at the hemoglobin α1β1 subunit interface , 1986 .

[8]  C. Chothia,et al.  Hydrophobic bonding and accessible surface area in proteins , 1974, Nature.

[9]  S. Kim,et al.  Solvent-accessible surfaces of nucleic acids. , 1979, Journal of molecular biology.

[10]  E. Padlan,et al.  Antibody-antigen complexes. , 1988, Annual review of biochemistry.

[11]  J M Blaney,et al.  A geometric approach to macromolecule-ligand interactions. , 1982, Journal of molecular biology.

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

[13]  I. Kuntz,et al.  Docking flexible ligands to macromolecular receptors by molecular shape. , 1986, Journal of medicinal chemistry.

[14]  Peter A. Kollman,et al.  AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions , 1981 .

[15]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.

[16]  A Wlodawer,et al.  Comparison of two highly refined structures of bovine pancreatic trypsin inhibitor. , 1987, Journal of molecular biology.

[17]  D. Chandler,et al.  Theory of the hydrophobic effect , 1977 .

[18]  Trajectory simulation studies of diffusion-controlled reactions. , 1987, Faraday discussions of the Chemical Society.

[19]  J. Warwicker,et al.  Investigating protein-protein interaction surfaces using a reduced stereochemical and electrostatic model. , 1989, Journal of molecular biology.

[20]  A. Shrake,et al.  Environment and exposure to solvent of protein atoms. Lysozyme and insulin. , 1973, Journal of molecular biology.

[21]  J. Morrison,et al.  Methotrexate, a high-affinity pseudosubstrate of dihydrofolate reductase. , 1979, Biochemistry.

[22]  M. Lewis,et al.  Fractal surfaces of proteins. , 1985, Science.

[23]  F M Richards,et al.  Areas, volumes, packing and protein structure. , 1977, Annual review of biophysics and bioengineering.

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

[25]  N. Xuong,et al.  Dihydrofolate reductase from Lactobacillus casei. X-ray structure of the enzyme methotrexate.NADPH complex. , 1978, Journal of Biological Chemistry.

[26]  P. Pfeifer,et al.  Fractal surface dimension of proteins: Lysozyme , 1985 .

[27]  T. Richmond,et al.  Solvent accessible surface area and excluded volume in proteins. Analytical equations for overlapping spheres and implications for the hydrophobic effect. , 1984, Journal of molecular biology.

[28]  M. L. Connolly Analytical molecular surface calculation , 1983 .

[29]  I. Kuntz,et al.  Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure. , 1988, Journal of medicinal chemistry.

[30]  Frederic M. Richards,et al.  Packing of α-helices: Geometrical constraints and contact areas☆ , 1978 .

[31]  R. Huber,et al.  The Geometry of the Reactive Site and of the Peptide Groups in Trypsin, Trypsinogen and its Complexes with Inhibitors , 1983 .

[32]  O. Tapia,et al.  Surface fractality as a guide for studying protein—protein interactions , 1987 .

[33]  A M Lesk,et al.  Interior and surface of monomeric proteins. , 1987, Journal of molecular biology.

[34]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[35]  S H Northrup,et al.  Brownian dynamics of cytochrome c and cytochrome c peroxidase association. , 1988, Science.

[36]  R Diamond,et al.  Real-space refinement of the structure of hen egg-white lysozyme. , 1977, Journal of molecular biology.

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

[38]  M. Levitt,et al.  Energy refinement of hen egg-white lysozyme. , 1974, Journal of molecular biology.

[39]  J. Mccammon,et al.  Simulation of the diffusion‐controlled reaction between superoxide and superoxide dismutase. II. Detailed models , 1985, Biopolymers.

[40]  D. K. Friesen,et al.  A combinatorial algorithm for calculating ligand binding , 1984 .

[41]  L. Johnson,et al.  Structure of Some Crystalline Lysozyme-Inhibitor Complexes Determined by X-Ray Analysis At 6 Å Resolution , 1965, Nature.

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