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1
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Calculations of electrostatic interactions in biological systems and in solutions
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Warshel A, Russell ST. Calculations of electrostatic interactions in biological systems and in solutions. Q Rev Biophys. 17:1984;283-422.
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Warshel, A.1
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Roles of electrostatic interaction in proteins
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Nakamura H. Roles of electrostatic interaction in proteins. Q Rev Biophys. 29:1996;1-90.
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Nakamura, H.1
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Electrostatic basis of structure - Function correlation in proteins
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Warshel A. Electrostatic basis of structure - function correlation in proteins. Accounts Chem Res. 14:1981;284-290.
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Accounts Chem Res
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Warshel, A.1
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Electrostatic interactions in macromolecules: Theory and applications
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Sharp KA, Honig B. Electrostatic interactions in macromolecules: theory and applications. Annu Rev Biophys Biophys Chem. 19:1990;301-332.
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Sharp, K.A.1
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Electrostatic energy and macromolecular function
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Warshel A, Åqvist J. Electrostatic energy and macromolecular function. Annu Rev Biophys Biophys Chem. 20:1991;267-298.
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Theory of electrostatic interactions in macromolecules
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Gilson MK. Theory of electrostatic interactions in macromolecules. Curr Opin Struct Biol. 5:1995;216-223.
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Gilson, M.K.1
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PH-dependence of protein stability: Absolute electrostatic free energy differences between conformations
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Schaefer M, Sommer M, Karplus M. pH-dependence of protein stability: absolute electrostatic free energy differences between conformations. J Phys Chem B. 101:1997;1663-1683.
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Schaefer, M.1
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Ewald summation versus direct summation of shifted-force potentials for the calculation of electrostatic interactions in solids - A quantitative study
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Dufner H, Kast SM, Brickmann J, Schlenkrich M. Ewald summation versus direct summation of shifted-force potentials for the calculation of electrostatic interactions in solids - a quantitative study. J Comput Chem. 18:1997;660-676.
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Dufner, H.1
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Figueirido F, Delbuono GS, Levy RM. On finite-size corrections to the free-energy of ionic hydration. J Phys Chem B. 101:1997;5622-5623.
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A local reaction field method for fast evaluation of long-range electrostatic interactions in molecular simulations
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Lee FS, Warshel A. A local reaction field method for fast evaluation of long-range electrostatic interactions in molecular simulations. J Chem Phys. 97:1992;3100-3107.
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Lee, F.S.1
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12
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0001382020
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Calculation of absolute binding free-energies for charged ligands and effects of long-range electrostatic interactions
-
of special interest. The absolute binding free energies of charged ligands are evaluated using an innovative variant of the LRA treatment of [15] and the LRF treatment [11]. This LRA variant neglects the average over the configuration generated with the uncharged solute and estimates the hydrophobic contribution by scaling the average van der Waals contribution (this contribution is evaluated in [15] by the PDLD surface area estimate). This paper pays significant attention to the importance of the proper treatment of long-range effects, clearly illustrating the superiority of the LRF treatment over cut-off methods. The problems associated with FEP approaches are also illustrated clearly.
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Aqvist J. Calculation of absolute binding free-energies for charged ligands and effects of long-range electrostatic interactions. of special interest J Comput Chem. 17:1996;1587-1597 The absolute binding free energies of charged ligands are evaluated using an innovative variant of the LRA treatment of [15] and the LRF treatment [11]. This LRA variant neglects the average over the configuration generated with the uncharged solute and estimates the hydrophobic contribution by scaling the average van der Waals contribution (this contribution is evaluated in [15] by the PDLD surface area estimate). This paper pays significant attention to the importance of the proper treatment of long-range effects, clearly illustrating the superiority of the LRF treatment over cut-off methods. The problems associated with FEP approaches are also illustrated clearly.
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Aqvist, J.1
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13
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Free energy of charges in solvated proteins: Microscopic calculations using a reversible charging process
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Warshel A, Sussman F, King G. Free energy of charges in solvated proteins: microscopic calculations using a reversible charging process. Biochemistry. 25:1986;8368-8372.
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Biochemistry
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Warshel, A.1
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14
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Free-energy calculations - Applications to chemical and biochemical phenomena
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Kollman P. Free-energy calculations - applications to chemical and biochemical phenomena. Chem Rev. 93:1993;2395-2417.
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Kollman, P.1
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0026596911
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Calculations of antibody antigen interactions - Microscopic and semimicroscopic evaluation of the free-energies of binding of phosphorylcholine analogs to McPC603
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Lee FS, Chu ZT, Bolger MB, Warshel A. Calculations of antibody antigen interactions - microscopic and semimicroscopic evaluation of the free-energies of binding of phosphorylcholine analogs to McPC603. Protein Eng. 5:1992;215-228.
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Protein Eng
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Lee, F.S.1
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16
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-
0028169692
-
as of ionizable residues in proteins - An explicit solvent calculation for lysozyme
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as of ionizable residues in proteins - an explicit solvent calculation for lysozyme. Proteins. 20:1994;85-97.
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Proteins
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Del Buono, G.S.1
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New method for predicting binding affinity in computer-aided drug design
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Aqvist J, Medina C, Samuelsson J-E. New method for predicting binding affinity in computer-aided drug design. Protein Eng. 7:1994;385-391.
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Protein Eng
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Aqvist, J.1
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18
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0030604609
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The static dielectric-constant of the soft sticky dipole model of liquid water - Monte-Carlo simulation
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Liu Y, Ichiye T. The static dielectric-constant of the soft sticky dipole model of liquid water - Monte-Carlo simulation. Chem Phys Lett. 256:1996;334-340.
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Liu, Y.1
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Coalson RD, Duncan A. Statistical mechanics of a multipolar gas: a lattice field theory approach. J Phys Chem. 100:1996;2612-2620.
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Coalson, R.D.1
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Continuum and dipole-lattice models of solvation
-
note
-
Papazyan A, Warshel A. Continuum and dipole-lattice models of solvation. of special interest J Phys Chem B. 101:1997;11254-11264 The connection between discrete and continuum representations of solvation is made in a concrete manner. New insights into the meaning and domain of applicability of the Clausius - Mossotti equation are revealed. The insufficiency of capturing the macroscopic dielectric constant for solvation behavior is demonstrated, with implications for cut-off schemes in molecular simulations. Further validation of the Langevin dipoles model is provided by its essentially exact agreement with the more 'realistic' Brownian dipole model at a given dielectric constant. A novel way of obtaining the 'microscopic' dielectric constants is devised, which involves a pointwise comparison of microscopic electric polarization and potential with the numerical solution of the Poisson equation. The fact that the continuum dielectric is the infinite dipole density limit of a more general dipole-lattice description is shown by recovering the continuum results with dipole lattices of high number density. The linearity of the continuum models is explained as a direct consequence of being the infinite density limit of a dipolar model.
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J Phys Chem B
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Papazyan, A.1
Warshel, A.2
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22
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0031276965
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A stringent test of the cavity concept in continuum dielectrics
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Papazyan A, Warshel A. A stringent test of the cavity concept in continuum dielectrics. J Chem Phys. 107:1997;7975-7978.
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J Chem Phys
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Papazyan, A.1
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24
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0021480222
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Macroscopic models for studies of electrostatic interactions in proteins: Limitations and applicability
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Warshel A, Russell ST, Churg AK. Macroscopic models for studies of electrostatic interactions in proteins: limitations and applicability. Proc Natl Acad Sci USA. 81:1984;4785-4789.
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Proc Natl Acad Sci USA
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Warshel, A.1
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25
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0028859420
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Conformation and hydrogen-ion titration of proteins - A continuum electrostatic model with conformational flexibility
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You TJ, Bashford D. Conformation and hydrogen-ion titration of proteins - a continuum electrostatic model with conformational flexibility. Biophys J. 69:1995;1721-1733.
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You, T.J.1
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26
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0029665693
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as in proteins
-
note
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eff. At any rate, the null model is not really a predictive model in the sense that it only 'predicts' the trivial cases in which the protein does very little; as argued in the text and [24], these are not the interesting cases.
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Antosiewicz, J.1
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0344778061
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Semianalytical treatment of solvation for molecular mechanics and dynamics
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St WC II, Tempozyk A, Hawley RC, Hendrickson T. Semianalytical treatment of solvation for molecular mechanics and dynamics. J Am Chem Soc. 112:1990;6127-6129.
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St W.C. II1
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0031075977
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Solvation free energies of peptides: Comparison of approximate continuum solvation models with accurate solution of the Poisson - Boltzmann equation
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note
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Edinger SR, Cortis C, Shenkin PS, Friesner RA. Solvation free energies of peptides: comparison of approximate continuum solvation models with accurate solution of the Poisson - Boltzmann equation. of special interest J Phys Chem B. 101:1997;1190-1197 An attempt at a systematic comparison of several simplified models of solvation. Readers must be warned, however, about a couple of shortcomings: it singles out the GB model as an approximation for the PB equation or a solution of the multicavity continuum model, implying that the other models are not. In fact, none of the compared models are rigorously derived from the PB equation, and all of them can be regarded as an 'approximation' to the PB equation. However, a good solvation model does not necessarily aim to approximate PB equation which is itself an approximation to the real solvation behavior. GB is the mathematical statement of the empirically observed behavior of a pair of charges in homogeneous solutions. As such, it is a good solvation model within its domain of applicability, namely uniform dielectrics. Despite the implication in this paper, GB is no more valid than a distance-dependent dielectric (DDD) model, when the latter is properly parametrized based on empirical data (just as GB is parametrized). GB and DDD models have been shown to be equivalent [1,41,85].
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J Phys Chem B
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Edinger, S.R.1
Cortis, C.2
Shenkin, P.S.3
Friesner, R.A.4
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0000357781
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Calculations of chemical processes in solutions
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Warshel A. Calculations of chemical processes in solutions. J Phys Chem. 83:1979;1640-16542.
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Warshel, A.1
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0001029719
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On finite-size effects in computer simulations using the Ewald potential
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Figueirido F, Delbuono GS, Levy RM. On finite-size effects in computer simulations using the Ewald potential. J Chem Phys. 103:1995;6133-6142.
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0030134110
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On the validity of electrostatic linear-response in polar solvents
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Åqvist J, Hansson T. On the validity of electrostatic linear-response in polar solvents. J Phys Chem. 100:1996;9512-9521.
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Generalized linear-response approximation in discrete methods
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Orozco M, Luque FJ. Generalized linear-response approximation in discrete methods. Chem Phys Lett. 265:1997;473-480.
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33
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0031187388
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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
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Florian J, Warshel A. 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. J Phys Chem B. 101:1997;5583-5595.
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J Phys Chem B
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Florian, J.1
Warshel, A.2
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84962418523
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Assessment of the Langevin dipoles solvation model for Hartree - Fock wave-functions
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Malcolm NOJ, McDouall JJW. Assessment of the Langevin dipoles solvation model for Hartree - Fock wave-functions. J Mol Struct. 366:1996;1-9.
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New model for calculation of solvation free energies: Correction of self-consistent reaction field continuum dielectric theory for short-range hydrogen-bonding effects
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Marten B, Kim K, Cortis C, Friesner RA, Murphy RB, Ringnalda MN, Sitkoff D, Honig B. New model for calculation of solvation free energies: correction of self-consistent reaction field continuum dielectric theory for short-range hydrogen-bonding effects. J Phys Chem. 100:1996;11775-11788.
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Marten, B.1
Kim, K.2
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Friesner, R.A.4
Murphy, R.B.5
Ringnalda, M.N.6
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Honig, B.8
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36
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-
0003100369
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Quantum mechanical models for reactions in solution
-
G. Náray-Szabó, Warshel A. Dordrecht, The Netherlands: Kluwer Academic Publishers
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Tomasi J, Mennucci B, Cammi R, Cossi M. Quantum mechanical models for reactions in solution. Náray-Szabó G, Warshel A. Computational Approaches to Biochemical Reactivity. 1997;1-102 Kluwer Academic Publishers, Dordrecht, The Netherlands.
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Tomasi, J.1
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37
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33748390341
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Parametrized models of aqueous free-energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium
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Hawkins GD, Cramer CJ, Truhlar DG. Parametrized models of aqueous free-energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium. J Phys Chem. 100:1996;19824-19839.
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Hawkins, G.D.1
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Truhlar, D.G.3
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38
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0029410817
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Structure-energy analysis of the role of metal ion in phosphodiester bond hydrolysis by DNA polymerase I
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Fothergill M, Goodman MF, Petruska J, Warshel A. Structure-energy analysis of the role of metal ion in phosphodiester bond hydrolysis by DNA polymerase I. J Am Chem Soc. 117:1995;11619-11627.
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J Am Chem Soc
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Fothergill, M.1
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Petruska, J.3
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39
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0029989997
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Computer simulation of the trisephosphate isomerase catalyzed reaction
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Åqvist J, Fothergill M. Computer simulation of the trisephosphate isomerase catalyzed reaction. J Biol Chem. 271:1996;10010-10016.
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0347657860
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Saito M. Molecular dynamics free-energy study of a protein in solution with all degrees of freedom and long-range Coulomb interactions. J Phys Chem. 99:1995;17043-17048.
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Saito, M.1
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41
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0000703443
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Self-consistent, free energy based approximation to calculate pH dependent electrostatic effects in proteins
-
of special interest. This paper outlines the relationship between the Lorentz - Debye - Sack theory of solvation and a DDD model. It shows that the latter is equivalent to the GB method.
-
Mehler EL. Self-consistent, free energy based approximation to calculate pH dependent electrostatic effects in proteins. of special interest J Phys Chem. 100:1996;16006-16018 This paper outlines the relationship between the Lorentz - Debye - Sack theory of solvation and a DDD model. It shows that the latter is equivalent to the GB method.
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Mehler, E.L.1
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0030970306
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Self-consistent field approach to protein structure and stability. 1. pH-dependence of electrostatic contribution
-
as, but this is due to the fact that the method results in a large effective dielectric constant for charge - charge interactions. In this sense, the use of a large dielectric constant is not much different than the approach used in [24]; however, here and in many related studies, the crucial self-energy (i.e. solvation) contribution is overlooked and charge - charge interactions are mistakenly assumed to be the main electrostatic effects. This along with the assumption that insensitivity to ionic strength implies a diminished importance of electrostatics are two important misconceptions that still surface in current literature.
-
as, but this is due to the fact that the method results in a large effective dielectric constant for charge - charge interactions. In this sense, the use of a large dielectric constant is not much different than the approach used in [24]; however, here and in many related studies, the crucial self-energy (i.e. solvation) contribution is overlooked and charge - charge interactions are mistakenly assumed to be the main electrostatic effects. This along with the assumption that insensitivity to ionic strength implies a diminished importance of electrostatics are two important misconceptions that still surface in current literature.
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Proteins
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Dimitrov, R.A.1
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Lamm G, Pack GR. Calculation of dielectric constants near polyelectrolytes in solution. J Phys Chem B. 101:1997;959-965.
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Svensson B, Jonsson B. An efficient simulation technique for electrostatic free-energies with applications to azurin. J Comput Chem. 16:1995;370-377.
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Zhou H-X. Control of reduction potential by protein matrix: lesson from a spherical protein model. J Biol Inorg Chem. 2:1997;109-113.
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Zhou H-X1
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Control of metalloprotein redox potentials: What does site-directed mutagenesis of hemoproteins tell us?
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Mauk AG, Moore GR. Control of metalloprotein redox potentials: what does site-directed mutagenesis of hemoproteins tell us? J Biol Inorg Chem. 2:1997;119-125.
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Mauk, A.G.1
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The importance of the protein in controlling the electrochemistry of heme metalloproteins: Methods of calculation and analysis
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Gunner MR, Alexov E, Torres E, Lipovaca S. The importance of the protein in controlling the electrochemistry of heme metalloproteins: methods of calculation and analysis. J Biol Inorg Chem. 2:1997;126-134.
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Gunner, M.R.1
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Electrostatic modulation of electron transfer in the active site of heme peroxidases
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Náray-Szabó G. Electrostatic modulation of electron transfer in the active site of heme peroxidases. J Biol Inorg Chem. 2:1997;135-138.
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Evaluations of reduction potential data in relation to coupling, kinetics and function
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Armstrong FA. Evaluations of reduction potential data in relation to coupling, kinetics and function. J Biol Inorg Chem. 2:1997;139-142.
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Armstrong, F.A.1
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53
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Microscopic and semimacroscopic redox calculations: What can and cannot be learned from continuum models
-
Warshel A, Papazyan A, Muegge I. Microscopic and semimacroscopic redox calculations: what can and cannot be learned from continuum models. J Biol Inorg Chem. 2:1997;143-152.
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J Biol Inorg Chem
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Warshel, A.1
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54
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0030828226
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The reorganization energy of cytochrome-c revisited
-
of special interest. The experimentally observed structural changes upon oxidation of cytochrome c are coverted to reorganization energy using different microscopic and macroscopic models. The results provide a structure based estimate of the activation barrier for electron transfer between two cytochromes, and establish that different dielectric constants are associated with different models.
-
Muegge I, Qi PX, Wand AJ, Chu ZT, Warshel A. The reorganization energy of cytochrome-c revisited. of special interest J Phys Chem B. 101:1997;825-836 The experimentally observed structural changes upon oxidation of cytochrome c are coverted to reorganization energy using different microscopic and macroscopic models. The results provide a structure based estimate of the activation barrier for electron transfer between two cytochromes, and establish that different dielectric constants are associated with different models.
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J Phys Chem B
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Muegge, I.1
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Kassner RJ. Effects of nonpolar environments on the redox potentials of heme proteins. Proc Natl Acad Sci USA. 69:1972;2263-2267.
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-
Kassner, R.J.1
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56
-
-
0023044641
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Control of redox potential of cytochrome c and microscopic dielectric effects in proteins
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Churg AK, Warshel A. Control of redox potential of cytochrome c and microscopic dielectric effects in proteins. Biochemistry. 25:1986;1675-1681.
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(1986)
Biochemistry
, vol.25
, pp. 1675-1681
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-
Churg, A.K.1
Warshel, A.2
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57
-
-
0001531848
-
Protein control of redox potentials of iron-sulfur proteins
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Stephens PJ, Jollie DR, Warshel A. Protein control of redox potentials of iron-sulfur proteins. Chem Rev. 96:1996;2491-2513.
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(1996)
Chem Rev
, vol.96
, pp. 2491-2513
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-
Stephens, P.J.1
Jollie, D.R.2
Warshel, A.3
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58
-
-
0029753015
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Structural origins of redox potentials in Fe-S proteins - Electrostatic potentials of crystal structures
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Swartz PD, Beck BW, Ichiye T. Structural origins of redox potentials in Fe-S proteins - electrostatic potentials of crystal structures. Biophys J. 71:1996;2958-2969.
-
(1996)
Biophys J
, vol.71
, pp. 2958-2969
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-
Swartz, P.D.1
Beck, B.W.2
Ichiye, T.3
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59
-
-
0029188718
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Calculations of electrostatic energies in photosynthetic reaction centers
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Alden RG, Parson WW, Chu ZT, Warshel A. Calculations of electrostatic energies in photosynthetic reaction centers. J Am Chem Soc. 117:1995;12284-12298.
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(1995)
J Am Chem Soc
, vol.117
, pp. 12284-12298
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-
Alden, R.G.1
Parson, W.W.2
Chu, Z.T.3
Warshel, A.4
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60
-
-
0000936310
-
Solvation free-energy reaction curves for electron-transfer in aqueous solution - Theory and simulation
-
Yelle RB, Ichiye T. Solvation free-energy reaction curves for electron-transfer in aqueous solution - theory and simulation. J Phys Chem B. 101:1997;4127-4135.
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(1997)
J Phys Chem B
, vol.101
, pp. 4127-4135
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-
Yelle, R.B.1
Ichiye, T.2
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61
-
-
0010042667
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Binding of azide to human carbonic anydrase II. The role electrostatic complementarity plays in selecting the preferred resonance structure of azide
-
Merz KM, Banci L. Binding of azide to human carbonic anydrase II. The role electrostatic complementarity plays in selecting the preferred resonance structure of azide. J Phys Chem. 100:1996;17414-17420.
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(1996)
J Phys Chem
, vol.100
, pp. 17414-17420
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-
Merz, K.M.1
Banci, L.2
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62
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-
0346496058
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Calculations of the electrostatic free-energy contributions to the binding free-energy of sulfonamides to carbonic-anhydrase
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Madura JD, Nakajima Y, Hamilton RM, Wierzbicki A, Warshel A. Calculations of the electrostatic free-energy contributions to the binding free-energy of sulfonamides to carbonic-anhydrase. Struct Chem. 7:1996;131-138.
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(1996)
Struct Chem
, vol.7
, pp. 131-138
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-
Madura, J.D.1
Nakajima, Y.2
Hamilton, R.M.3
Wierzbicki, A.4
Warshel, A.5
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63
-
-
0030584674
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Electrostatic control of GTP and GDP binding in the oncoprotein P21(ras)
-
Muegge I, Schweins T, Langer R, Warshel A. Electrostatic control of GTP and GDP binding in the oncoprotein P21(ras). Structure. 4:1996;475-489.
-
(1996)
Structure
, vol.4
, pp. 475-489
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-
Muegge, I.1
Schweins, T.2
Langer, R.3
Warshel, A.4
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64
-
-
0031404601
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A fast estimate of electrostatic group contributions to the free energy of protein-inhibitor binding
-
Muegge I, Tao H, Warshel A. A fast estimate of electrostatic group contributions to the free energy of protein-inhibitor binding. Protein Eng. 10:1998;1363-1372.
-
(1998)
Protein Eng
, vol.10
, pp. 1363-1372
-
-
Muegge, I.1
Tao, H.2
Warshel, A.3
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65
-
-
85005693432
-
Effective methods for estimation of binding energies in computer-aided drug design
-
Warshel A, Tao H, Fothergill M, Chu ZT. Effective methods for estimation of binding energies in computer-aided drug design. Isr J Chem. 34:1994;253-256.
-
(1994)
Isr J Chem
, vol.34
, pp. 253-256
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-
Warshel, A.1
Tao, H.2
Fothergill, M.3
Chu, Z.T.4
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66
-
-
0031008575
-
On the calculation of binding free-energies using continuum methods - Application to MHC class-1 protein - Peptide interactions
-
of special interest. Binding free energies of peptides to proteins are evaluated by the Poisson - Boltzmann method, using the charging cycle introduced in earlier PDLD/S studies [15]; however, current results are still not satisfactory both in terms of the observed trends and absolute values.
-
Froloff N, Windemuth A, Honig B. On the calculation of binding free-energies using continuum methods - application to MHC class-1 protein - peptide interactions. of special interest Protein Sci. 6:1997;1293-1301 Binding free energies of peptides to proteins are evaluated by the Poisson - Boltzmann method, using the charging cycle introduced in earlier PDLD/S studies [15]; however, current results are still not satisfactory both in terms of the observed trends and absolute values.
-
(1997)
Protein Sci
, vol.6
, pp. 1293-1301
-
-
Froloff, N.1
Windemuth, A.2
Honig, B.3
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67
-
-
0031547977
-
Empirical free energy calculations - A blind test and further improvements to the method
-
Novotny J, Bruccoleri RE, Davis M, Sharp KA. Empirical free energy calculations - a blind test and further improvements to the method. J Mol Biol. 268:1997;401-411.
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(1997)
J Mol Biol
, vol.268
, pp. 401-411
-
-
Novotny, J.1
Bruccoleri, R.E.2
Davis, M.3
Sharp, K.A.4
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68
-
-
0032031405
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Electrostatic contributions to protein - Protein binding affinities: Application to Rap/Raf interaction
-
Muegge I, Schweins T, Warshel A. Electrostatic contributions to protein - protein binding affinities: application to Rap/Raf interaction. Proteins. 30:1998;407-423.
-
(1998)
Proteins
, vol.30
, pp. 407-423
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-
Muegge, I.1
Schweins, T.2
Warshel, A.3
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69
-
-
0031547966
-
Electrostatic complementarity at protein/protein interfaces
-
Mccoy AJ, Epa VC, Colman PM. Electrostatic complementarity at protein/protein interfaces. J Mol Biol. 268:1997;570-584.
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(1997)
J Mol Biol
, vol.268
, pp. 570-584
-
-
McCoy, A.J.1
Epa, V.C.2
Colman, P.M.3
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70
-
-
0003006336
-
Electrostatic basis of enzyme catalysis
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G. Náray-Szabó, Warshel A. Dordrecht, The Netherlands: Kluwer Academic Publishers
-
Náray-Szabó G, Fuxreiter M, Warshel A. Electrostatic basis of enzyme catalysis. Náray-Szabó G, Warshel A. Computational Approaches to Biochemical Reactivity. 1997;237-294 Kluwer Academic Publishers, Dordrecht, The Netherlands.
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(1997)
Computational Approaches to Biochemical Reactivity
, pp. 237-294
-
-
Náray-Szabó, G.1
Fuxreiter, M.2
Warshel, A.3
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71
-
-
0031022260
-
The contribution of electrostatic and van-der-Waals interactions to the stereospecificity of the reaction catalyzed by lactate-dehydrogenase
-
Van Beek J, Callender R, Gunner MR. The contribution of electrostatic and van-der-Waals interactions to the stereospecificity of the reaction catalyzed by lactate-dehydrogenase. Biophys J. 72:1997;619-626.
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(1997)
Biophys J
, vol.72
, pp. 619-626
-
-
Van Beek, J.1
Callender, R.2
Gunner, M.R.3
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72
-
-
0030929123
-
Computational, pulse-radiolytic, and structural investigations of lysine-136 and its role in the electrostatic triad of human Cu, Zn superoxide dismutase
-
Fisher CL, Cabelli DE, Hallewell RA, Beroza P, Lo TP, Getzoff ED, Tainer JA. Computational, pulse-radiolytic, and structural investigations of lysine-136 and its role in the electrostatic triad of human Cu, Zn superoxide dismutase. Proteins. 29:1997;103-112.
-
(1997)
Proteins
, vol.29
, pp. 103-112
-
-
Fisher, C.L.1
Cabelli, D.E.2
Hallewell, R.A.3
Beroza, P.4
Lo, T.P.5
Getzoff, E.D.6
Tainer, J.A.7
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74
-
-
84962422582
-
On the origin of the catalytic power of acetylcholinesterase: Computer simulation studies
-
Fuxreiter M, Warshel A. On the origin of the catalytic power of acetylcholinesterase: computer simulation studies. J Am Chem Soc. 120:1997;183-194.
-
(1997)
J Am Chem Soc
, vol.120
, pp. 183-194
-
-
Fuxreiter, M.1
Warshel, A.2
-
75
-
-
0029833224
-
Boundary conditions for single-ion diffusion
-
+ through the gramicidin channel. This is done by comparing the calculated and observed conductance. It is found that the barriers calculated by the approach of Roux and Karplus [76] drastically overestimate the actual barrier whereas the profile obtained by Åqvist and Warshel [77] is more realistic. Although the authors are hesitant to criticize [76] and point out that a scaling factor of ~0.3 gives 'excellent' agreement with experiments, the fact remains that seemingly rigorous potential-of-mean-force force treatments, when used with an improper treatment of long-range interactions, produces incorrect penetration barriers (which are the most important factors in controlling ion conductance).
-
+ through the gramicidin channel. This is done by comparing the calculated and observed conductance. It is found that the barriers calculated by the approach of Roux and Karplus [76] drastically overestimate the actual barrier whereas the profile obtained by Åqvist and Warshel [77] is more realistic. Although the authors are hesitant to criticize [76] and point out that a scaling factor of ~0.3 gives 'excellent' agreement with experiments, the fact remains that seemingly rigorous potential-of-mean-force force treatments, when used with an improper treatment of long-range interactions, produces incorrect penetration barriers (which are the most important factors in controlling ion conductance).
-
(1996)
Biophys J
, vol.71
, pp. 1723-1742
-
-
McGill, P.1
Schumaker, M.F.2
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76
-
-
0027232024
-
Ion transport in the gramicidin channel: Free energy of the solvated right-handed dimer in a model membrane
-
Roux B, Karplus M. Ion transport in the gramicidin channel: free energy of the solvated right-handed dimer in a model membrane. J Am Chem Soc. 115:1993;3250-3262.
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(1993)
J Am Chem Soc
, vol.115
, pp. 3250-3262
-
-
Roux, B.1
Karplus, M.2
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78
-
-
0030050164
-
A semimicroscopic Monte Carlo study of permeation energetics in a gramicidin-like channel - The origin of selectivity
-
Dorman V, Partenskii MB, Jordan PC. A semimicroscopic Monte Carlo study of permeation energetics in a gramicidin-like channel - the origin of selectivity. Biophys J. 70:1996;121-134.
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(1996)
Biophys J
, vol.70
, pp. 121-134
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-
Dorman, V.1
Partenskii, M.B.2
Jordan, P.C.3
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79
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0029757155
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Binding of small basic peptides to membranes containing acidic lipids - Theoretical models and experimental results
-
Ben Tal N, Honig B, Peitzsch RM, Denisov G. Binding of small basic peptides to membranes containing acidic lipids - theoretical models and experimental results. Biophys J. 71:1996;561-575.
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(1996)
Biophys J
, vol.71
, pp. 561-575
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-
Ben Tal, N.1
Honig, B.2
Peitzsch, R.M.3
Denisov, G.4
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80
-
-
0001143764
-
Molecular dynamics simulation of immobilized artificial membranes
-
Sheng Q, Schulten K, Pidgeon C. Molecular dynamics simulation of immobilized artificial membranes. J Phys Chem. 99:1995;11018-11027.
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(1995)
J Phys Chem
, vol.99
, pp. 11018-11027
-
-
Sheng, Q.1
Schulten, K.2
Pidgeon, C.3
-
81
-
-
0000083584
-
Microscopic simulations of macroscopic dielectric constants of solvated proteins
-
King G, Lee FS, Warshel A. Microscopic simulations of macroscopic dielectric constants of solvated proteins. J Chem Phys. 95:1991;4366-4377.
-
(1991)
J Chem Phys
, vol.95
, pp. 4366-4377
-
-
King, G.1
Lee, F.S.2
Warshel, A.3
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82
-
-
0029833446
-
Charge screening and the dielectric-constant of proteins - Insights from molecular dynamics
-
Simonson T, Brooks CL. Charge screening and the dielectric-constant of proteins - insights from molecular dynamics. J Am Chem Soc. 118:1996;8452-8458.
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(1996)
J Am Chem Soc
, vol.118
, pp. 8452-8458
-
-
Simonson, T.1
Brooks, C.L.2
-
83
-
-
0010624785
-
The effect of protein relaxation on charge - Charge interactions and dielectric constants in proteins
-
in press
-
Sham YY, Muegge I, Warshel A. The effect of protein relaxation on charge - charge interactions and dielectric constants in proteins. Biophys J. 1998;. in press.
-
(1998)
Biophys J
-
-
Sham, Y.Y.1
Muegge, I.2
Warshel, A.3
-
84
-
-
0030945495
-
Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties
-
Alexov EG, Gunner MR. Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties. Biophys J. 72:1997;2075-2093.
-
(1997)
Biophys J
, vol.72
, pp. 2075-2093
-
-
Alexov, E.G.1
Gunner, M.R.2
-
85
-
-
84986466995
-
Microscopic models for quantum mechanical calculations of chemical processes in solution
-
Luzhkov V, Warshel A. Microscopic models for quantum mechanical calculations of chemical processes in solution. J Comput Chem. 13:1992;199-213.
-
(1992)
J Comput Chem
, vol.13
, pp. 199-213
-
-
Luzhkov, V.1
Warshel, A.2
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