The statistical-thermodynamic basis for computation of binding affinities: a critical review.
暂无分享,去创建一个
M. Gilson | J. Mccammon | J. Given | B. Bush | J. McCammon
[1] W. G. McMillan,et al. The Statistical Thermodynamics of Multicomponent Systems , 1945 .
[2] G. E. Myers,et al. Low molecular weight proteins. Thermodynamics of the association of insulin molecules , 1953 .
[3] Theory of Protein Solutions. II , 1955 .
[4] T. L. Hill. Theory of Protein Solutions. I , 1955 .
[5] Thermodynamics for Chemists and Chemical Engineers , 1956, Nature.
[6] C. Tanford,et al. Theory of Protein Titration Curves. I. General Equations for Impenetrable Spheres , 1957 .
[7] W. Kauzmann. Some factors in the interpretation of protein denaturation. , 1959, Advances in protein chemistry.
[8] H. Scheraga,et al. Entropy changes accompanying association reactions of proteins. , 1963, The Journal of biological chemistry.
[9] B. Widom,et al. Some Topics in the Theory of Fluids , 1963 .
[10] V. Shcherbakov. Neighbor interactions and exchange of ligands , 1964 .
[11] J. Wyman,et al. THE BINDING POTENTIAL, A NEGLECTED LINKAGE CONCEPT. , 1965, Journal of molecular biology.
[12] J. E. Prue. Ion pairs and complexes: Free energies, enthalpies, and entropies , 1969 .
[13] W. Jencks,et al. Entropic contributions to rate accelerations in enzymic and intramolecular reactions and the chelate effect. , 1971, Proceedings of the National Academy of Sciences of the United States of America.
[14] H. C. Andersen. Cluster expansions for hydrogen‐bonded fluids. I. Molecular association in dilute gases , 1973 .
[15] J. Schellman,et al. Macromolecular binding , 1975 .
[16] C. Chothia,et al. Principles of protein–protein recognition , 1975, Nature.
[17] A. Ben-Naim. Solute and solvent effects on chemical equilibria , 1975 .
[18] Jean-Claude Justice,et al. Ionic interactions in solutions. I. The association concepts and the McMillan-Mayer theory , 1976 .
[19] C. Chothia,et al. Role of hydrophobicity in the binding of coenzymes. Appendix. Translational and rotational contribution to the free energy of dissociation. , 1978, Biochemistry.
[20] K. Olaussen,et al. Statistical mechanical model with chemical reaction , 1980 .
[21] R. Jaenicke,et al. Reversible high-pressure dissociation of lactic dehydrogenase from pig muscle. , 1980, Biochemistry.
[22] R. Jaenicke,et al. Kinetics of reconstitution of porcein muscle lactic dehydrogenase after reversible high pressure dissociation. , 1980, Biophysical Chemistry.
[23] E Morild,et al. The theory of pressure effects on enzymes. , 1981, Advances in protein chemistry.
[24] R. Jaenicke,et al. Pressure-induced structural changes of pig heart lactic dehydrogenase. , 1981, Biophysical chemistry.
[25] B. Widom,et al. Potential-distribution theory and the statistical mechanics of fluids , 1982 .
[26] A. Szabó,et al. Role of diffusion in ligand binding to macromolecules and cell-bound receptors. , 1982, Biophysical journal.
[27] M. Wertheim,et al. Fluids with highly directional attractive forces. I. Statistical thermodynamics , 1984 .
[28] David J. Craik,et al. FUNCTIONAL GROUP CONTRIBUTIONS TO DRUG-RECEPTOR INTERACTIONS , 1985 .
[29] F. Gurd,et al. pH-dependent processes in proteins. , 1985, CRC critical reviews in biochemistry.
[30] J. Hermans,et al. The Free Energy of Xenon Binding to Myoglobin from Molecular Dynamics Simulation , 1986 .
[31] J. A. McCammon,et al. Dynamics and Design of Enzymes and Inhibitors. , 1986 .
[32] A. D. McLachlan,et al. Solvation energy in protein folding and binding , 1986, Nature.
[33] M. Wertheim,et al. Fluids with highly directional attractive forces. III. Multiple attraction sites , 1986 .
[34] P. A. Bash,et al. Free energy calculations by computer simulation. , 1987, Science.
[35] K. Pitzer,et al. The restricted primitive model for ionic fluids , 1987 .
[36] Martin Karplus,et al. A thermodynamic analysis of solvation , 1988 .
[37] J. Andrew McCammon,et al. Quantum simulation of ferrocytochrome c , 1988, Nature.
[38] William L. Jorgensen,et al. Efficient computation of absolute free energies of binding by computer simulations. Application to the methane dimer in water , 1988 .
[39] Harold A. Scheraga,et al. Free energies of hydration of solute molecules. IV: Revised treatment of the hydration shell model , 1988 .
[40] Yaoqi Zhou,et al. Chemical association in simple models of molecular and ionic fluids , 1989 .
[41] C L Brooks,et al. Thermodynamics of amide hydrogen bond formation in polar and apolar solvents. , 1989, Journal of molecular biology.
[42] A V Finkelstein,et al. The price of lost freedom: entropy of bimolecular complex formation. , 1989, Protein engineering.
[43] D. Beveridge,et al. Free energy via molecular simulation: applications to chemical and biomolecular systems. , 1989, Annual review of biophysics and biophysical chemistry.
[44] Activation and Reaction Volumes in Solution. Part 2. , 1989 .
[45] H. Erickson,et al. Co-operativity in protein-protein association. The structure and stability of the actin filament. , 1989, Journal of molecular biology.
[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] T. Steinmetzer,et al. Design of Enzyme Inhibitors as Drugs , 1989 .
[48] M. Karplus,et al. pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model. , 1990, Biochemistry.
[49] H. Corti,et al. The cluster theory for electrolyte solutions. Its extension and its limitations , 1990 .
[50] J M Blaney,et al. Molecular modeling software and methods for medicinal chemistry. , 1990, Journal of medicinal chemistry.
[51] Nissim Claude Cohen,et al. Molecular Modeling Software and Methods for Medicinal Chemistry , 1990 .
[52] W. C. Still,et al. Semianalytical treatment of solvation for molecular mechanics and dynamics , 1990 .
[53] S. Freer,et al. Design of enzyme inhibitors using iterative protein crystallographic analysis. , 1991, Journal of medicinal chemistry.
[54] William L. Jorgensen,et al. Monte Carlo simulations yield absolute free energies of binding for guanine—cytosine and adenine—uracil base pairs in chloroform , 1991 .
[55] J. Andrew McCammon,et al. Free energy difference calculations by thermodynamic integration: Difficulties in obtaining a precise value , 1991 .
[56] R. D. Groot. The association constant of a flexible molecule and a single atom: Theory and simulation , 1992 .
[57] M. Lewis,et al. Calculation of the free energy of association for protein complexes , 1992, Protein science : a publication of the Protein Society.
[58] P. Kollman,et al. Molecular dynamics studies of calixspherand complexes with alkali metal cations: calculation of the absolute and relative free energies of binding of cations to a calixspherand , 1992 .
[59] Dudley H. Williams,et al. Partitioning of free energy contributions in the estimation of binding constants : Residual motions and consequences for amide-amide hydrogen bond strengths , 1992 .
[60] P A Kollman,et al. Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches , 1993, Proteins.
[61] K. P. Murphy,et al. Structural energetics of peptide recognition: Angiotensin II/antibody binding , 1993, Proteins.
[62] P A Kollman,et al. What determines the strength of noncovalent association of ligands to proteins in aqueous solution? , 1993, Proceedings of the National Academy of Sciences of the United States of America.
[63] B Honig,et al. On the pH dependence of protein stability. , 1993, Journal of molecular biology.
[64] C. Sander,et al. An effective solvation term based on atomic occupancies for use in protein simulations , 1993 .
[65] Reply to the comment on "Entropy of hydrophobic hydration: a new statistical mechanical formulation" , 1993 .
[66] W. Braun,et al. Surface area included in energy refinement of proteins. A comparative study on atomic solvation parameters. , 1993, Journal of molecular biology.
[67] Peter A. Kollman,et al. FREE ENERGY CALCULATIONS : APPLICATIONS TO CHEMICAL AND BIOCHEMICAL PHENOMENA , 1993 .
[68] M. Gilson. Multiple‐site titration and molecular modeling: Two rapid methods for computing energies and forces for ionizable groups in proteins , 1993, Proteins.
[69] J J Baldwin,et al. Application of the three-dimensional structures of protein target molecules in structure-based drug design. , 1994, Journal of medicinal chemistry.
[70] K. P. Murphy,et al. Entropy in biological binding processes: Estimation of translational entropy loss , 1994, Proteins.
[71] M Karplus,et al. The contribution of vibrational entropy to molecular association. The dimerization of insulin. , 1994, Journal of molecular biology.
[72] D. Beglov,et al. Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations , 1994 .
[73] Thomas Simonson,et al. Solvation Free Energies Estimated from Macroscopic Continuum Theory: An Accuracy Assessment , 1994 .
[74] Rainer Jaenicke,et al. Proteins under pressure , 1994 .
[75] P. Colman,et al. Structure-based drug design. , 1994, Current opinion in structural biology.
[76] Equilibrium polymerization and gelation. I. Integral‐equation theory , 1994 .
[77] Arieh Warshel,et al. Effective Methods for Estimation of Binding Energies in Computer‐Aided Drug Design , 1994 .
[78] I. Kuntz,et al. Structure-Based Molecular Design , 1994 .
[79] Hans-Joachim Böhm,et al. The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure , 1994, J. Comput. Aided Mol. Des..
[80] R. S. Spolar,et al. Coupling of local folding to site-specific binding of proteins to DNA. , 1994, Science.
[81] Alexandre Varnek,et al. An application of the Miertus‐Scrocco‐Tomasi solvation model in molecular mechanics and dynamics simulations , 1995, J. Comput. Chem..
[82] A. Holtzer. The “cratic correction” and related fallacies , 1995, Biopolymers.
[83] Ajay,et al. Computational methods to predict binding free energy in ligand-receptor complexes. , 1995, Journal of medicinal chemistry.
[84] B. Matthews,et al. Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme. , 1995, Biochemistry.
[85] S Vajda,et al. Flexible docking and design. , 1995, Annual review of biophysics and biomolecular structure.
[86] J Hermans,et al. Hydrophilicity of cavities in proteins , 1996, Proteins.
[87] S Vajda,et al. Prediction of protein complexes using empirical free energy functions , 1996, Protein science : a publication of the Protein Society.
[88] Jeremy C. Smith,et al. Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study. , 1996, Biophysical journal.
[89] N. Ben-Tal,et al. Statistical thermodynamic analysis of peptide and protein insertion into lipid membranes. , 1996, Biophysical journal.
[90] P. Rossky,et al. Size Dependence of Transfer Free Energies. 2. Hard Sphere Models , 1996 .
[91] J. Andrew McCammon,et al. Comparison of Continuum and Explicit Models of Solvation: Potentials of Mean Force for Alanine Dipeptide , 1996 .
[92] J. Briggs,et al. Structure-based drug design: computational advances. , 1997, Annual review of pharmacology and toxicology.
[93] R. Eldik,et al. Activation and Reaction Volumes in Solution. 3. , 1978, Chemical reviews.