A new class of models for computing receptor-ligand binding affinities.
暂无分享,去创建一个
[1] A. W. Rosenbluth,et al. MONTE CARLO CALCULATION OF THE AVERAGE EXTENSION OF MOLECULAR CHAINS , 1955 .
[2] J. Wyman,et al. THE BINDING POTENTIAL, A NEGLECTED LINKAGE CONCEPT. , 1965, Journal of molecular biology.
[3] C. Chothia,et al. Principles of protein–protein recognition , 1975, Nature.
[4] M. Kröger,et al. Influence of different levels of 2-thiocytidine on physical and template properties of cytidine--2-thiocytidine copolymers. , 1979, Biochemistry.
[5] J. E. McQueen,et al. Energy minimizations of rubredoxin. , 1980, Journal of molecular biology.
[6] M. Karplus,et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .
[7] U. Singh,et al. A NEW FORCE FIELD FOR MOLECULAR MECHANICAL SIMULATION OF NUCLEIC ACIDS AND PROTEINS , 1984 .
[8] P. Andrews,et al. Functional group contributions to drug-receptor interactions. , 1984, Journal of medicinal chemistry.
[9] H. Berendsen,et al. A consistent empirical potential for water–protein interactions , 1984 .
[10] F. Gurd,et al. pH-dependent processes in proteins. , 1985, CRC critical reviews in biochemistry.
[11] J. Andrew McCammon,et al. Dynamics and design of enzymes and inhibitors , 1986 .
[12] A. D. McLachlan,et al. Solvation energy in protein folding and binding , 1986, Nature.
[13] A. Warshel,et al. Free energy of charges in solvated proteins: microscopic calculations using a reversible charging process. , 1986, Biochemistry.
[14] P. A. Bash,et al. Free energy calculations by computer simulation. , 1987, Science.
[15] B. Honig,et al. Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis , 1988, Proteins.
[16] Kenny B. Lipkowitz,et al. Protocol for determining enantioselective binding of chiral analytes on chiral chromatographic surfaces , 1988 .
[17] Harold A. Scheraga,et al. Free energies of hydration of solute molecules. IV: Revised treatment of the hydration shell model , 1988 .
[18] D. Beveridge,et al. Free energy via molecular simulation: applications to chemical and biomolecular systems. , 1989, Annual review of biophysics and biophysical chemistry.
[19] H. Erickson,et al. Co-operativity in protein-protein association. The structure and stability of the actin filament. , 1989, Journal of molecular biology.
[20] R. Bruccoleri,et al. On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3, and HyHEL-5. , 1989, Biochemistry.
[21] K. Lipkowitz,et al. Theoretical studies in molecular recognition: Rebek's cleft , 1989 .
[22] M. Karplus,et al. pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model. , 1990, Biochemistry.
[23] W. C. Still,et al. Semianalytical treatment of solvation for molecular mechanics and dynamics , 1990 .
[24] S. Freer,et al. Design of enzyme inhibitors using iterative protein crystallographic analysis. , 1991, Journal of medicinal chemistry.
[25] Ronald M. Levy,et al. Gaussian fluctuation formula for electrostatic free‐energy changes in solution , 1991 .
[26] Kenneth M. Merz,et al. Determination of pKas of ionizable groups in proteins: The pKa of Glu 7 and 35 in hen egg white lysozyme and Glu 106 in human carbonic anhydrase II , 1991 .
[27] Jenn-Huei Lii,et al. The MM3 force field for amides, polypeptides and proteins , 1991 .
[28] J. Andrew McCammon,et al. Free energy difference calculations by thermodynamic integration: Difficulties in obtaining a precise value , 1991 .
[29] M. Lewis,et al. Calculation of the free energy of association for protein complexes , 1992, Protein science : a publication of the Protein Society.
[30] Berend Smit,et al. Novel scheme to study structural and thermal properties of continuously deformable molecules , 1992 .
[31] 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 .
[32] K. Sharp,et al. Macroscopic models of aqueous solutions : biological and chemical applications , 1993 .
[33] K. P. Murphy,et al. Structural energetics of peptide recognition: Angiotensin II/antibody binding , 1993, Proteins.
[34] C. Sander,et al. An effective solvation term based on atomic occupancies for use in protein simulations , 1993 .
[35] D. Theodorou,et al. A concerted rotation algorithm for atomistic Monte Carlo simulation of polymer melts and glasses , 1993 .
[36] N. Allewell,et al. Multigrid solution of the nonlinear Poisson-Boltzmann equation and calculation of titration curves. , 1993, Biophysical journal.
[37] K. Sharp,et al. On the calculation of pKas in proteins , 1993, Proteins.
[38] Peter A. Kollman,et al. FREE ENERGY CALCULATIONS : APPLICATIONS TO CHEMICAL AND BIOCHEMICAL PHENOMENA , 1993 .
[39] M. Gilson. Multiple‐site titration and molecular modeling: Two rapid methods for computing energies and forces for ionizable groups in proteins , 1993, Proteins.
[40] Norman L. Allinger,et al. Molecular mechanics parameters , 1994 .
[41] PatrickY.-S. Lam,et al. Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors. , 1994, Science.
[42] Malcolm E. Davis,et al. The inducible multipole solvation model: A new model for solvation effects on solute electrostatics , 1994 .
[43] Ming-Jing Hwang,et al. Derivation of Class II Force Fields. 2. Derivation and Characterization of a Class II Force Field, CFF93, for the Alkyl Functional Group and Alkane Molecules , 1994 .
[44] D. Beglov,et al. Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations , 1994 .
[45] Arieh Warshel,et al. Effective Methods for Estimation of Binding Energies in Computer‐Aided Drug Design , 1994 .
[46] M. Gilson,et al. Prediction of pH-dependent properties of proteins. , 1994, Journal of molecular biology.
[47] 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..
[48] Ming-Jing Hwang,et al. Derivation of Class II Force Fields. III. Characterization of a Quantum Force Field for Alkanes , 1994 .
[49] Ming-Jing Hwang,et al. Derivation of class II force fields. I. Methodology and quantum force field for the alkyl functional group and alkane molecules , 1994, J. Comput. Chem..
[50] Alexander D. MacKerell,et al. pH dependence of binding reactions from free energy simulations and macroscopic continuum electrostatic calculations: application to 2'GMP/3'GMP binding to ribonuclease T1 and implications for catalysis. , 1995, Journal of molecular biology.
[51] Alexis T. Bell,et al. Sorption Thermodynamics, Siting, and Conformation of Long n-Alkanes in Silicalite As Predicted by Configurational-Bias Monte Carlo Integration , 1995 .
[52] E. Purisima,et al. Calculation of relative binding free energies and configurational entropies: a structural and thermodynamic analysis of the nature of non-polar binding of thrombin inhibitors based on hirudin55-65. , 1995, Journal of molecular biology.
[53] Ajay,et al. Computational methods to predict binding free energy in ligand-receptor complexes. , 1995, Journal of medicinal chemistry.
[54] B. Matthews,et al. Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme. , 1995, Biochemistry.
[55] Freeman J. Dyson,et al. The same and not the same , 1995 .
[56] Thomas A. Halgren,et al. Merck molecular force field. IV. conformational energies and geometries for MMFF94 , 1996 .
[57] Michael W. Deem,et al. A configurational bias Monte Carlo method for linear and cyclic peptides , 1996, cond-mat/9709330.
[58] S. Subramaniam,et al. Explicit solvent models in protein pKa calculations. , 1996, Biophysical journal.
[59] Thomas A. Halgren,et al. Merck molecular force field. III. Molecular geometries and vibrational frequencies for MMFF94 , 1996, J. Comput. Chem..
[60] E. Mehler. Self-Consistent, Free Energy Based Approximation To Calculate pH Dependent Electrostatic Effects in Proteins , 1996 .
[61] S Vajda,et al. Prediction of protein complexes using empirical free energy functions , 1996, Protein science : a publication of the Protein Society.
[62] T. Halgren. Merck molecular force field. II. MMFF94 van der Waals and electrostatic parameters for intermolecular interactions , 1996 .
[63] Jenn-Huei Lii,et al. An improved force field (MM4) for saturated hydrocarbons , 1996, J. Comput. Chem..
[64] Enrico O. Purisima,et al. Analysis of thermodynamic determinants in helix propensities of nonpolar amino acids through a novel free energy calculation , 1996 .
[65] Rebecca C. Wade,et al. Improving the Continuum Dielectric Approach to Calculating pKas of Ionizable Groups in Proteins , 1996 .
[66] T. Halgren,et al. Merck molecular force field. V. Extension of MMFF94 using experimental data, additional computational data, and empirical rules , 1996 .
[67] T. Halgren. Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94 , 1996, J. Comput. Chem..
[68] M. Gilson. Modeling protonation equilibria in biomolecules , 1997 .
[69] Michael K. Gilson,et al. ''Mining minima'': Direct computation of conformational free energy , 1997 .
[70] J. Briggs,et al. Structure-based drug design: computational advances. , 1997, Annual review of pharmacology and toxicology.
[71] M. Gilson,et al. The statistical-thermodynamic basis for computation of binding affinities: a critical review. , 1997, Biophysical journal.