Electrostatic effects in macromolecules: fundamental concepts and practical modeling.
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[1] A. McCoy,et al. Electrostatic complementarity at protein/protein interfaces. , 1997, Journal of molecular biology.
[2] W. C. Still,et al. Semianalytical treatment of solvation for molecular mechanics and dynamics , 1990 .
[3] A. Warshel,et al. Microscopic and semimacroscopic redox calculations: what can and cannot be learned from continuum models , 1997, JBIC Journal of Biological Inorganic Chemistry.
[4] J Novotny,et al. Empirical free energy calculations: a blind test and further improvements to the method. , 1997, Journal of molecular biology.
[5] M K Gilson,et al. Theory of electrostatic interactions in macromolecules. , 1995, Current opinion in structural biology.
[6] H. Dufner,et al. Ewald summation versus direct summation of shifted‐force potentials for the calculation of electrostatic interactions in solids: A quantitative study , 1997 .
[7] F. J. Luque,et al. Generalized linear response approximation in discrete methods , 1997 .
[8] F. Armstrong. Evaluations of reduction potential data in relation to coupling, kinetics and function , 1997, JBIC Journal of Biological Inorganic Chemistry.
[9] R. Levy,et al. Intrinsic pKas of ionizable residues in proteins: An explicit solvent calculation for lysozyme , 1994, Proteins.
[10] P. Beroza,et al. Computational, pulse‐radiolytic, and structural investigations of lysine‐136 and its role in the electrostatic triad of human C u,Z n superoxide dismutase , 1997, Proteins.
[11] Yi Liu,et al. The static dielectric constant of the soft sticky dipole model of liquid water: Monte Carlo simulation , 1996 .
[12] T. Ichiye,et al. Solvation Free Energy Reaction Curves for Electron Transfer in Aqueous Solution: Theory and Simulation , 1997 .
[13] Arieh Warshel,et al. Microscopic simulations of macroscopic dielectric constants of solvated proteins , 1991 .
[14] J. Åqvist,et al. Computer Simulation of the Triosephosphate Isomerase Catalyzed Reaction (*) , 1996, The Journal of Biological Chemistry.
[15] G. Náray‐Szabó. Electrostatic modulation of electron transfer in the active site of heme peroxidases , 1997, JBIC Journal of Biological Inorganic Chemistry.
[16] P McGill,et al. Boundary conditions for- single-ion diffusion. , 1996, Biophysical journal.
[17] A. Warshel,et al. Control of the redox potential of cytochrome c and microscopic dielectric effects in proteins. , 1986, Biochemistry.
[18] T. Hansson,et al. On the Validity of Electrostatic Linear Response in Polar Solvents , 1996 .
[19] E. Alexov,et al. Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties. , 1997, Biophysical journal.
[20] K. Merz,et al. Binding of Azide to Human Carbonic Anhydrase II: The Role Electrostatic Complementarity Plays in Selecting the Preferred Resonance Structure of Azide , 1996 .
[21] Arieh Warshel,et al. The Reorganization Energy of Cytochrome c Revisited , 1997 .
[22] Arieh Warshel,et al. CONTINUUM AND DIPOLE-LATTICE MODELS OF SOLVATION , 1997 .
[23] K. Schulten,et al. Molecular Dynamic Simulation of Immobilized Artificial Membranes , 1995 .
[24] J. McDouall,et al. Assessment of the Langevin dipoles solvation model for Hartree-Fock wavefunctions , 1996 .
[25] A. Warshel,et al. Electrostatic contributions to protein–protein binding affinities: Application to Rap/Raf interaction , 1998, Proteins.
[26] Charles L. Brooks,et al. CHARGE SCREENING AND THE DIELECTRIC CONSTANT OF PROTEINS : INSIGHTS FROM MOLECULAR DYNAMICS , 1996 .
[27] Arieh Warshel,et al. Microscopic models for quantum mechanical calculations of chemical processes in solutions: LD/AMPAC and SCAAS/AMPAC calculations of solvation energies , 1992 .
[28] Arieh Warshel,et al. Effective Methods for Estimation of Binding Energies in Computer‐Aided Drug Design , 1994 .
[29] Bo Svensson,et al. An efficient simulation technique for electrostatic free energies with applications to azurin , 1995, J. Comput. Chem..
[30] Peter A. Kollman,et al. FREE ENERGY CALCULATIONS : APPLICATIONS TO CHEMICAL AND BIOCHEMICAL PHENOMENA , 1993 .
[31] Huan-Xiang Zhou,et al. Control of reduction potential by protein matrix: lesson from a spherical protein model , 1997, JBIC Journal of Biological Inorganic Chemistry.
[32] Rob D. Coalson,et al. Statistical Mechanics of a Multipolar Gas: A Lattice Field Theory Approach , 1996 .
[33] A. Warshel,et al. How do serine proteases really work? , 1989, Biochemistry.
[34] C. Luchinat,et al. Are unit charges always negligible? , 1997, JBIC Journal of Biological Inorganic Chemistry.
[35] J. Aqvist,et al. A new method for predicting binding affinity in computer-aided drug design. , 1994, Protein engineering.
[36] A. Warshel,et al. Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603. , 1992, Protein engineering.
[37] A. Warshel,et al. A fast estimate of electrostatic group contributions to the free energy of protein-inhibitor binding. , 1997, Protein engineering.
[38] Tony J. You,et al. Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility. , 1995, Biophysical journal.
[39] Martin Karplus,et al. pH-Dependence of Protein Stability: Absolute Electrostatic Free Energy Differences between Conformations† , 1997 .
[40] Calculations of the electrostatic free energy contributions to the binding free energy of sulfonamides to carbonic anhydrase , 1996 .
[41] A. Warshel,et al. The effect of protein relaxation on charge-charge interactions and dielectric constants of proteins. , 1998, Biophysical journal.
[42] E. Mehler. Self-Consistent, Free Energy Based Approximation To Calculate pH Dependent Electrostatic Effects in Proteins , 1996 .
[43] A. Warshel,et al. Electrostatic control of GTP and GDP binding in the oncoprotein p21ras. , 1996, Structure.
[44] M. Gilson,et al. Simulation of charge-mutant acetylcholinesterases. , 1995, Biochemistry.
[45] R. G. Alden,et al. Calculations of Electrostatic Energies in Photosynthetic Reaction Centers , 1995 .
[46] Ronald M. Levy,et al. On finite‐size effects in computer simulations using the Ewald potential , 1995 .
[47] Gerhard Hummer,et al. Free Energy of Ionic Hydration , 1996 .
[48] Gregory D. Hawkins,et al. Parametrized Models of Aqueous Free Energies of Solvation Based on Pairwise Descreening of Solute Atomic Charges from a Dielectric Medium , 1996 .
[49] A. Warshel,et al. Calculations of electrostatic interactions in biological systems and in solutions , 1984, Quarterly Reviews of Biophysics.
[50] A. Warshel,et al. A STRINGENT TEST OF THE CAVITY CONCEPT IN CONTINUUM DIELECTRICS , 1997 .
[51] A. Warshel,et al. Free energy of charges in solvated proteins: microscopic calculations using a reversible charging process. , 1986, Biochemistry.
[52] A. Warshel,et al. Electrostatic energy and macromolecular function. , 1991, Annual review of biophysics and biophysical chemistry.
[53] J. Åqvist,et al. Calculation of absolute binding free energies for charged ligands and effects of long‐range electrostatic interactions , 1996 .
[54] A. Warshel,et al. Structure-energy analysis of the role of metal ions in phosphodiester bond hydrolysis by DNA polymerase I , 1995 .
[55] Arieh Warshel,et al. Consistent Calculations of pKa's of Ionizable Residues in Proteins: Semi-microscopic and Microscopic Approaches , 1997 .
[56] G. Moore,et al. Control of metalloprotein redox potentials: what does site-directed mutagenesis of hemoproteins tell us? , 1997, JBIC Journal of Biological Inorganic Chemistry.
[57] Peter C. Jordan,et al. A semi-microscopic Monte Carlo study of permeation energetics in a gramicidin-like channel: the origin of cation selectivity. , 1996, Biophysical journal.
[58] B. Honig,et al. New Model for Calculation of Solvation Free Energies: Correction of Self-Consistent Reaction Field Continuum Dielectric Theory for Short-Range Hydrogen-Bonding Effects , 1996 .
[59] Arieh Warshel,et al. Langevin Dipoles Model for ab Initio Calculations of Chemical Processes in Solution: Parametrization and Application to Hydration Free Energies of Neutral and Ionic Solutes and Conformational Analysis in Aqueous Solution , 1997 .
[60] J. V. van Beek,et al. The contribution of electrostatic and van der Waals interactions to the stereospecificity of the reaction catalyzed by lactate dehydrogenase. , 1997, Biophysical journal.
[61] S. Linse,et al. Measurement and modelling of sequence-specific pKa values of lysine residues in calbindin D9k. , 1996, Journal of molecular biology.
[62] A. Warshel,et al. Macroscopic models for studies of electrostatic interactions in proteins: limitations and applicability. , 1984, Proceedings of the National Academy of Sciences of the United States of America.
[63] T. Ichiye,et al. Structural origins of redox potentials in Fe-S proteins: electrostatic potentials of crystal structures. , 1996, Biophysical journal.
[64] Arieh Warshel,et al. Protein Control of Redox Potentials of Iron−Sulfur Proteins , 1996 .
[65] H. Nakamura,et al. Roles of electrostatic interaction in proteins , 1996, Quarterly Reviews of Biophysics.
[66] Minoru Saito,et al. Molecular dynamics/free energy study of a protein in solution with all degrees of freedom and long-range Coulomb interactions , 1995 .
[67] M. Gilson,et al. The determinants of pKas in proteins. , 1996, Biochemistry.
[68] A. Warshel,et al. Origin of the catalytic power of acetylcholinesterase: Computer simulation studies , 1998 .
[69] M. Karplus,et al. Ion transport in the gramicidin channel: free energy of the solvated right-handed dimer in a model membrane , 1993 .
[70] B Honig,et al. On the calculation of binding free energies using continuum methods: Application to MHC class I protein‐peptide interactions , 1997, Protein science : a publication of the Protein Society.
[71] K. Sharp,et al. Electrostatic interactions in macromolecules: theory and applications. , 1990, Annual review of biophysics and biophysical chemistry.
[72] G. Lamm,et al. Calculation of Dielectric Constants near Polyelectrolytes in Solution , 1997 .
[73] R. Dimitrov,et al. Self‐consistent field approach to protein structure and stability. i: pH dependenceof electrostatic contribution , 1997, Proteins.
[74] Arieh Warshel,et al. A local reaction field method for fast evaluation of long‐range electrostatic interactions in molecular simulations , 1992 .
[75] A. Warshel. Electrostatic basis of structure-function correlation in proteins , 1981 .
[76] A. Warshel,et al. Energetics of ion permeation through membrane channels. Solvation of Na+ by gramicidin A. , 1989, Biophysical journal.
[77] Ronald M. Levy,et al. On Finite-Size Corrections to the Free Energy of Ionic Hydration , 1997 .
[78] Richard A. Friesner,et al. Solvation Free Energies of Peptides: Comparison of Approximate Continuum Solvation Models with Accurate Solution of the Poisson−Boltzmann Equation , 1997 .
[79] E. Lattman,et al. Experimental measurement of the effective dielectric in the hydrophobic core of a protein. , 1997, Biophysical chemistry.
[80] Arieh Warshel,et al. Calculations of chemical processes in solutions , 1979 .
[81] B Honig,et al. Binding of small basic peptides to membranes containing acidic lipids: theoretical models and experimental results. , 1996, Biophysical journal.