Arieh warshel



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  1. Semiclassical Simulations of the Spectra of Anharmonic Molecules; Problems and Alternatives, J-K Hwang and A. Warshel, Chem. Phys. Lett. 115, 281-285 (1985).




  1. A Shortcut for Multidimensional Quantization. The Average Partial Action Methods, J-K Hwang and A. Warshel, Chem. Phys. Lett. 118, 289-292 (1985).




  1. Calculations of Spectroscopic Properties of Bacterial Reaction Centers, W. W. Parson, A. Scherz and A. Warshel in Antennas and Reaction Centers of Photosynthetic Bacteria, ed. M. E. Michel-Beyerle, Springer-Verlag, Berlin, p. 122-130, (1985).




  1. Polarization Constraints in Molecular Dynamics Simulation of Aqueous Solutions: The Surface Constraint All Atom Solvent (SCAAS) Model, A. Warshel and G. King, Chem. Phys. Lett. 121, 124-129 (1985).




  1. Simulating Solvent and Dielectric Effects, A. Warshel and S.T. Russell in Molecular Dynamics and Protein Structure, ed. J. Herman, Polycrystal Book Service, Western Springs, Illinois, 23 (1985).




  1. Control of Redox Potential of Cytochrome c and Microscopic Dielectric Effects in Proteins, A. K. Churg and A. Warshel, Biochemistry 25, 1675-1681 (1986).




  1. Simulation of the Dynamics of Electron Transfer Reactions in Polar Solvents: Semiclassical Trajectories and Dispersed Polaron Approaches, A. Warshel and J-K Hwang, J. Chem. Phys. 84, 4938-4957 (1986).




  1. Towards Computer Aided Site-Directed Mutagenesis of Enzymes, A. Warshel and F. Sussman, Proc. Natl. Acad. Sci. USA 83, 3806-3810 (1986).




  1. Correlation Between Structure and Efficiency of Light-Induced Proton Pumps, A. Warshel, Method Enzymol. 127, 578-587 (1986).




  1. Theoretical Correlation of Structure and Energetics in the Catalytic Reaction of Trypsin, A. Warshel and S. Russell, J. Am. Chem. Soc. 108, 6569-6579 (1986).




  1. Free Energy of Charges in Solvated Proteins: Microscopic Calculations Using a Reversible Charging Process, A. Warshel, F. Sussman and G. King, Biochemistry 25 8368-8372 (1986).




  1. Computer Simulation of Enzymatic Reactions, A. Warshel, S. Russell and F. Sussman, Isr. J. Chem. 27, 217-224 (1986).




  1. Microscopic Examination of Free Energy Relationships for Electron Transfer in Polar Solvents, J-K. Hwang and A. Warshel, J. Am. Chem. Soc. 109, 715-720 (1987).




  1. Spectroscopic Properties of Photosynthetic Reaction Centers. 1. Theory. A. Warshel and W. W. Parson, J. Am. Chem. Soc. 109, 6143-6152 (1987).




  1. Spectroscopic Properties of Photosynthetic Reaction Centers. 2. Application of the Theory of Rhodopseudomonas Viridis, W. W. Parson and A. Warshel, J. Am. Chem. Soc. 109, 6152-6163 (1987).




  1. Activation Free Energies of Enzymatic Reactions, Simulations and Experiments, A. Warshel in Structure, Dynamics and Functions of Biomolecules, ed. A. Ehrenberg, R. Rigler, A. Graslund and L. Nilsson Springer-Verlag, p. 61-64 (1987).




  1. Calculations of Spectroscopic Properties and Electron Transfer Kinetics of Photosynthetic Bacterial Reaction Centers, W.W. Parson, S. Creighton, and A. Warshel in Primary Processes in Photobiology, ed. T Kobyashi, Springer-Verlag, p. 43 (1987).




  1. Simulating the Dynamics of Electron Transfer Reactions in Cytochrome c, A. Warshel in Protein Structure Molecular and Electronic Reactivity, ed. R. Austin, Springer-Verlag, p. 351 (1987).




  1. Semiquantitative Calculations of Catalytic Free Energies in Genetically Modified Enzymes, J. K. Hwang and A. Warshel, Biochemistry 26, 2669-2673 (1987).




  1. What about Protein Polarity, A. Warshel, (News and Views) Nature 330, 15-16 (1987).




  1. Simulating Rate Constants of Enzymatic Reactions and a Rational Engineering of Enzymes, F. Sussman and A. Warshel in Three Dimensional Structures and Drug Action ed. Y. Iiaka & A. Itai, University of Tokyo Press, 96 (1987).




  1. Simulating the Dynamics of the Primary Charge Separation Process in Bacterial Photosynthesis, S. Creighton, J-K Hwang, A. Warshel, W.W. Parson and J. Norris, Biochemistry 27, 774-781 (1988).




  1. Electron Transfer Pathways in The Primary Event of Bacterial Photosynthesis, A. Warshel, S. Creighton and W. W. Parson, J. Phys. Chem. 92, 2696-2701 (1988).




  1. Simulation of Free Energy Relationships and Dynamics of SN2 Reactions in Aqueous Solutions, J-K Hwang, G. King, S. Creighton and A. Warshel. J. Am. Chem. Soc. 110, 5297-5311 (1988).




  1. Effects of Solute-Solvent Coupling and Solvent Saturation on Solvation Dynamics of Charge Transfer Reactions. J-K Hwang, S. Creighton, G. King, D. Whitney, and A. Warshel, J. Chem. Phys. 89, 859-865 (1988).




  1. Simulating the Energetics and Dynamics of Enzymatic Reactions in Genetically Modified Enzymes, J-K Hwang, F. Sussman, and A. Warshel in Structure and Expression, ed. R. H Sarma and M. H. Sarma, Adenine Press, New York, p. 95-106 (1988).




  1. Why Ion-Pair Reversal by Protein Engineering is Unlikely to Succeed, J-K. Hwang and A. Warshel, Nature 334, 270-272 (1988).




  1. Evaluation of Catalytic Free Energies in Genetically Modified Proteins, A. Warshel, F. Sussman and J-K. Hwang, J. Mol. Biol. 201, 139-159 (1988).




  1. Spectroscopic Properties and Electron Transfer Dynamics of Reaction Centers, W. W. Parson, S. Creighton, A. Warshel and J. Norris in The Photosynthetic Bacterial Reaction Center, Structure and Dynamics, ed. J. Berton and A. Vermeglio. Plenuum Press, New York, 309 (1988).




  1. The Extended Ewald Method: A General Treatment of Long-Range Electrostatic Interactions in Microscopic Simulations, S. Kuwajima and A. Warshel, J. Chem. Phys. 89, 3751-3759 (1988).




  1. Microscopic Free Energy Calculations of Solvated Macromolecules as a Primary Structure-Function Correlator and the MOLARIS Program, A. Warshel and S. Creighton in Computer Simulation of Biomolecular Systems, W. F. van Gunsteren and P. K. Weiner, eds., ESCOM, Leiden, p. 120 (1989).




  1. How Do Serine Proteases Really Work? A. Warshel, G. Naray-Szabo, F. Sussman and J-K. Hwang, Biochemistry 28, 3629-3637 (1989).




  1. Energetics of Ion Permeation through Membrane Channels. The Solvation of Na+ by Gramicidin A, J. Åqvist and A. Warshel, Biophys. J. 56 171-182 (1989).




  1. Calculations of Free Energy Profiles for the Staphylococcal Nuclease Catalyzed Reaction, J. Åqvist and A. Warshel, Biochemistry 28, 4680-4689 (1989).




  1. Role of Arginine-38 in Regulation of the Cytochrome c Oxidation-Reduction Equilibrium, R.L. Cutler, A.M. Davies, S. Creighton, A. Warshel, G. R. Moore, M. Smith and A. G. Mauk, Biochemistry 28, 3188-3197 (1989).




  1. Calculations of Charge-Transfer Transition Energies and Spectroscopic Properties of a Molecular Crystal: Methylbacteriopheophorbide a, W. W. Parson, S. Creighton and A. Warshel, J. Am. Chem. Soc. 111, 4277-4284 (1989).




  1. Consistent Calculations of Electrostatic Free Energies in Membrane Channels. The Solvation of Na+ by the Gramicidin Channel, J. Åqvist and A. Warshel, Comments Mol. Cell. Biophys. 6, 91 (1989).




  1. Enzymes Work by Solvation Substitution Rather than by Desolvation. A. Warshel, J. Åqvist and S. Creighton, Proc. Natl. Acad. Sci. USA 86, 5820-5824 (1989).




  1. Microscopic Simulation of Quantum Dynamics and Nuclear Tunneling in Bacterial Reaction Centers. Z. T. Chu, A. Warshel and W. W. Parson, Photosynth. Res. 22, 39-46 (1989).




  1. Microscopic Simulations of Chemical Reactions in Solutions and Protein Active Sites; Principles and Examples, A. Warshel, in The Enzyme Catalysis Process, ed. A. Cooper, J. Houben and L. C. Chien, NATO ASI Series, Plenum Press, 178, 305-330 (1989).




  1. Electrostatic Correlation of Structure and Function in Proteins, A. Warshel and J. Åqvist, Nobel Symposium, Chemica Scripta, 29A, 75-83 (1989).




  1. Dispersed Polaron Simulations of Electron Transfer in Photosynthetic Reaction Centers, A. Warshel, Z. T. Chu and W. W. Parson, Science 246, 112-116 (1989).




  1. A Surface Constrained All-Atom Solvent Model for Effective Simulations of Polar Solutions, G. King and A. Warshel, J. Chem. Phys. 91, 3647-3661 (1989).




  1. Electrostatic Free Energy as the Fundamental Structure Function Correlation in Proteins. Some Perspectives from Microscopic Simulations of Protein Functions. A. Warshel, in Modeling of Molecular Structure and Properties, ed. J. L. Rivail, Studies in Physical and Theoretical Chemistry, Elsevier Science Publishers B. V. Amsterdam 71, 515-526 (1990).




  1. Incorporating Electric Polarizabilities in Water-Water Interaction Potentials, S. Kuwajima and A. Warshel, J. Phys. Chem. 94, 460-466 (1990).




  1. Free Energy Relationships in Metalloenzyme-Catalyzed Reactions. Calculations of the Effect of Metal Ion Substitutions in Staphylococcal Nuclease, J. Åqvist and A. Warshel, J. Am. Chem. Soc. 112, 2860-2868 (1990).




  1. Quantum Corrections for Rate Constants of Diabatic and Adiabatic Reactions in Solutions, A. Warshel and Z. T. Chu, J. Chem. Phys. 93, 4003-4015 (1990).




  1. Electrostatic Control of Charge Separation in Bacterial Photosynthesis, W.W. Parson, Z. T. Chu, and A. Warshel, BBA 1017, 251-272 (1990).




  1. Investigation of the Free Energy Functions for Electron Transfer Reactions, G. King and A. Warshel, J. Chem. Phys. 93, 8682-8692 (1990).




  1. Microscopic Simulations of Chemical Processes in Proteins and the Role of Electrostatic Free Energy, A. Warshel and J. Åqvist, in Theoretical Biochemistry and Molecular Biophysics, eds. D. L. Beveridge and R. Lavery, Adenine Press, Volume 2, p. 257-274.(1991).




  1. Electrostatic Energy and Macromolecular Function. A. Warshel and J. Åqvist, Annu. Rev. Biophys. Biophys. Chem. 20, 267-298 (1991).




  1. Dipoles Localized at Helix Termini of Proteins Stabilize Charges. J. Åqvist, H. Luecke, F. A. Quiocho, and A. Warshel, Proc. Natl. Acad. Sci. USA 88, 2026-2030 (1991).




  1. Role of Solvent Reorganization Energies in the Catalytic Activity of Enzymes. A. Yadav, R. M. Jackson, J. J. Holbrook and A. Warshel, J. Am. Chem. Soc. 113, 4800-4805 (1991).




  1. Microscopic Calculations of Solvent Effects on Absorption Spectra of Conjugated Molecules. V. Luzhkov and A. Warshel, J. Am. Chem. Soc. 113, 4491-4499 (1991).




  1. Computer Simulations of Electron Transfer Reactions in Solution and Photosynthetic Reaction Centers. A. Warshel, and W. W. Parson, Annu. Rev. Phys. Chem. 42, 279-309 (1991).




  1. Electrostatic Effects on the Speed and Directionality of Electron Transfer in Bacterial Reaction Centers: The Special Role of Tyrosine M-208. W. W. Parson, V. Nagarajan, D. Gaul, C. C. Schenck, Z.-T. Chu, and A. Warshel, in Reaction Centers of Photosynthetic Bacteria, ed. M.-E. Michel-Beyerle, Springer, Berlin, p. 239 (1991).




  1. Microscopic Simulations of Macroscopic Dielectric Constants of Solvated Proteins. G. King, F. S. Lee, and A. Warshel, J. Chem. Phys. 95, 4366-4377 (1991).




  1. Simulations of Quantum Mechanical Corrections for Rate Constants of Hydride-Transfer Reactions in Enzymes and Solutions. J.-K. Hwang, Z. T. Chu, A. Yadav, and A. Warshel, J. Phys. Chem. 95, 8445-8448 (1991).




  1. The Dynamics of the Primary Event in Rhodopsins Revisited, A. Warshel, Z. T. Chu and J.-K. Hwang, Chem. Phys. 158, 303-314 (1991).




  1. Calculations of Antibody-Antigen Interactions: Microscopic and Semi-Microscopic Evaluation of the Free Energies of Binding of Phosphorylcholine Analogs to McPC603, F. S. Lee, Z. T. Chu, M. B. Bolger, and A. Warshel, Protein Eng. 5, 215-228 (1992).




  1. Microscopic Models for Quantum Mechanical Calculations of Chemical Processes in Solutions: LD/AMPAC and SCAAS/AMPAC Calculations of Solvation Energies. V. Luzhkov and A. Warshel, J. Comput. Chem. 13, 199-213 (1992).




  1. Quantum-mechanical Calculations of Solvation Free Energies. A Combined ab initio Pseudopotential Free-energy Perturbation Approach. N. Vaidehi, T. A. Wesolowski, and A. Warshel, J. Chem. Phys. 97, 4264-4271 (1992).




  1. Computer Simulation of the Initial Proton Transfer Step in Human Carbonic Anhydrase I. J. Åqvist and A. Warshel, J. Mol. Biol. 224, 7-14 (1992).




  1. Computer Simulations of Enzymatic Reactions, A. Warshel, Curr. Opin. Struc. Biol. 2, 230-236 (1992).




  1. A Local Reaction Field Method for Fast Evaluation of Long-range Electrostatic Interactions in Molecular Simulations, F. S. Lee and A. Warshel, J. Chem. Phys. 97, 3100-3107 (1992).




  1. Computer Simulations of Enzymatic Reactions: Examination of Linear Free-energy Relationships and Quantum-mechanical Corrections in the Initial Proton-transfer Step of Carbonic Anhydrase, A. Warshel, J.-K. Hwang, J. Åqvist, Faraday Discuss. 93, 225-238 (1992).




  1. Effect of the Asn52Ile Mutation on the Redox Potent of Yeast Cytochrome C, R. Langen, G. D. Brayer, A.M. Berghuis, G. McLendon, F. Sherman and A. Warshel, J. Mol. Biol. 224, 589-600 (1992).




  1. Protein Control of Iron-Sulfur Cluster Redox Potentials, R. Langen, G. M. Jensen, U. Jacob, P. J. Stephens and A. Warshel, J. Biol. Chem. 267, No. 36, 25625-25627 (1992).




  1. On the Mechanism of Guanosine Triphosphate Hydrolysis in ras p21 Proteins. R. Langen, T. Schweins and A. Warshel, Biochemistry 31, 8691-8696 (1992).




  1. Simulations of Proton Transfer and Hydride Transfer Reactions in Proteins, A. Warshel, in Molecular Aspects of Biotechnology Computational Models and Theories, ed. J. Bertran, Kluwer Academic Publishers, Netherlands (1992).




  1. Computer Simulation of the CO2/HCO3- Interconversion Step in Human Carbonic Anhydrase I. J. Åqvist, M. Fothergill, A. Warshel, J. Am. Chem. Soc. 115, 631-635 (1993).




  1. Microscopic and Semimicroscopic Calculations of Electrostatic Energies in Proteins by the POLARIS and Enzymix Programs, F. S. Lee, Z. T. Chu, and A. Warshel, J. Comput. Chem. 14,161-185 (1993).




  1. Simulations of Electron Transfer in Bacterial Reaction Centers, W. W. Parson and A. Warshel, in The Photosynthetic Reaction Center, 2, ed. J. Norris and J. Deisenhofer Academic Press, Inc., p. 23 (1993).




  1. Molecule Recognition in the Catalytic Action of Metallo-Enzymes, J. Åqvist, and A. Warshel, in Principles of Molecular Recognition, ed. Buckingham, A. Legon and S. Robert, Blackie Academic Professional, p. 108-136 (1993).




  1. Frozen Density Functional Approach for Ab Initio Calculations of Solvated Molecules, T. A. Wesolowski and A. Warshel, J. Phys. Chem. 97, 8050-8053 (1993).




  1. Simulation of Enzyme Reactions Using Valence Bond Force Fields and Other Hybrid Quantum/Classical Approaches, J. Åqvist and A. Warshel, Chem. Rev. 93, 2523-2544 (1993).




  1. A Quantized Classical Path Approach for Calculations of Quantum Mechanical Rate Constants, J.-K. Hwang and A. Warshel, J. Phys. Chem. 97, 10053-10058 (1993).




  1. Chemical Shifts in Proteins: A Shielding Trajectory Analysis of the Fluorine Nuclear Magnetic Resonance Spectrum of the Escherichia coli Galactose Binding Protein Using a Multipole Shielding Polarizability-Local Reaction Field-Molecular Dynamics Approach, J. G. Pearson, E. Oldfield, F. S. Lee, A. Warshel, J. Am. Chem. Soc. 115, 6851-6862 (1993).




  1. On the Energetics of the Primary Electron-Transfer Process in Bacterial Reaction Centers, A. Warshel, Z. T. Chu, and W. W. Parson, J. Photoch. Photobio. A 82, 123-128 (1994).




  1. Theoretical Analyses of Electron-Transfer Reactions, W. W. Parson and A. Warshel, in Anoxygenic Photosynthetic Bacteria, ed. R. E. Blankenship, M. T. Madigan, and C. E. Bauer, Kluyer Academic Publishers (1994).




  1. Why Have Mutagenesis Studies Not Located the General Base in ras p21, T. Schweins, R. Langen and A. Warshel, Nat. Struct. Biol. 1, 476-484 (1994).




  1. Effective Methods for Estimation of Binding Energies in Computer-Aided Drug Design, A. Warshel, H. Tao, M. Fothergill and Z-T. Chu, Isr. J. Chem. 34, 253-256 (1994).




  1. Calculation of the Redox Potentials of Iron-Sulfur Proteins: the 2-/3-- Couple of [Fe4S4*Cys4] Clusters in Peptococcus aerogenes Ferredoxin, Azotobacter vinelandii Ferredoxin I, and Chromatium vinosum High-Potential Iron Protein, G. M. Jensen, A. Warshel and P. J. Stephens, Biochemistry 33, 10911-10924 (1994).




  1. Ab Initio Free Energy Perturbation Calculations of Solvation Free Energy Using the Frozen Density Functional Approach, T. Wesolowski and A. Warshel, J. Phys. Chem. 98, 5183-5187 (1994).




  1. Linear Free Energy Relationships in Enzymes. Theoretical Analysis of the Reaction of Tyrosyl-tRNA Synthetase, A. Warshel, T. Schweins and M. Fothergill, J. Am. Chem. Soc. 116, 8437-8442 (1994).




  1. Calculations of Solvation Free Energies in Chemistry and Biology, A. Warshel and Z. T. Chu, in ACS Symposium Series: Structure and Reactivity in Aqueous Solution: Characterization of Chemical and Biological Systems, ed. C. J. Cramer and D. G. Truhlar, 568, p. 71-94 (1994).




  1. Linear Free Energy Relationships with Quantum Mechanical Corrections: Classical and Quantum Mechanical Rate Constants for Hydride Transfer Between NAD+ Analogues in Solutions, Y. Kong and A. Warshel, J. Am. Chem. Soc. 117, 6234-6242 (1995).




  1. Substrate-Assisted Catalysis as a Mechanism for GTP Hydrolysis of p21ras and Other GTP-binding Proteins, T. Schweins, M. Geyer, K. Scheffzek, A. Warshel, H. R. Kalbitzer and A. Wittinghofer, Nat. Struct. Biol. 2, 36-44 (1995).




  1. On Low-Barrier Hydrogen Bonds and Enzyme Catalysis, A. Warshel, A. Papazyan and P. A. Kollman, Science 269, 102-104 (1995).




  1. Structure-Energy Analysis of the Role of Metal Ions in Phosphodiester Bond Hydrolysis by DNA Polymerase I, M. Fothergill, M. F. Goodman, J. Petruska and A. Warshel, J. Am. Chem. Soc. 117, No.47, 11619-11627 (1995).




  1. Ab Initio Calculations of Free Energy Barriers for Chemical Reactions in Solution, R. P. Muller and A. Warshel, J. Phys. Chem. 99, 17516-17524 (1995).




  1. Calculations of Electrostatic Energies in Photosynthetic Reaction Centers, R. G. Alden, W. W. Parson, Z. T. Chu and A. Warshel, J. Am. Chem. Soc. 117, 12284-12298 (1995).




  1. Ab Initio Calculations of Free Energy Barriers for Chemical Reactions in Solution: Proton Transfer in [FHF]-, R. P. Muller and A. Warshel, Pacific Symposium for Biocomputing. L. Hunter and T. E. Klein, eds. World Scientific Press, Singapore (1996).

  2. Macroscopic and Microscopic Estimates of the Energetics of Charge Separation in Bacterial Reaction Centers, R. G. Alden, W. W. Parson, Z. T. Chu and A. Warshel, in Reaction Centers of Photosynthetic Bacteria, Structure and Dynamics, ed. M. E. Michel-Beyerly, Springer-Verlag, Berlin (1996).




  1. Electrostatic Control of GTP and GDP Binding in the Oncoprotein p21ras, I. Muegge, T. Schweins, R. Langen and A. Warshel, Structure 4, 475-489 (1996).




  1. Calculations of the Electrostatic Free Energy Contributions to the Binding Free Energy of Sulfonamides to Carbonic Anhydrase, J. D. Madura, Y. Nakajima, R. M. Hamilton, A. Wierzbicki and A. Warshel, Struct. Chem. 7, 131-138 (1996).




  1. Energy Considerations Show that Low-Barrier Hydrogen Bonds Do Not Offer A Catalytic Advantage Over Ordinary Hydrogen Bonds, A. Warshel and A. Papazyan, Proc. Natl. Acad. Sci. USA 93, 13665-13670 (1996).




  1. Mechanistic Analysis of the Observed Linear Free Energy Relationships in p21ras and Related System, T. Schweins and A. Warshel, Biochemistry 35, 14232-14243 (1996).




  1. Linear Free Energy Relationships in the Intrinsic and GTPase Activating Protein-Stimulated Guanosine 5'-Triphosphate Hydrolysis of p21ras, T. Schweins, M. Geyer, H. R. Kalbitzer, A. Wittinghofer and A. Warshel, Biochemistry 35, 14225-14231 (1996).




  1. Protein Control of Redox Potentials of Iron-Sulfur Proteins, P. J. Stephens, D. R. Jollie and A. Warshel, Chem. Rev. 96, 2491-2513 (1996).




  1. How Important Are Quantum Mechanical Nuclear Motions in Enzyme Catalysis? J.-K. Hwang and A. Warshel, J. Am. Chem. Soc. 118, 11745-11751 (1996).




  1. Orientation of the OH Dipole of Tyrosine (M)210 and Its Effect on Electrostatic Energies in Photosynthetic Bacterial Reaction Centers, R. G. Alden, W. W. Parson, Z. T. Chu and A. Warshel, J. Phys. Chem. 100, 16761-16770 (1996).




  1. Ab Initio Frozen Density Functional Calculations of Proton Transfer Reactions in Solution, T. Wesolowski, R. P. Muller and A. Warshel, J. Phys. Chem. 100, 15444-15449 (1996).




  1. Calculations of Chemical Processes in Solution by Density Functional and Other Quantum Mechanical Techniques, R. P. Muller, T. Wesolowski and A. Warshel, in Density Functional Methods: Applications in Chemistry and Materials Science, ed. M. Springborg, John Wiley and Sons: p.189-206 (1997).




  1. Two-Dimensional Free Energy Surfaces for Primary Electron Transfer in a Photosynthetic Reaction Center, A. Warshel, Z. T. Chu and W. W. Parson, Chem. Phys. Lett. 265, 293-296 (1997).




  1. Microscopic and Semimacroscopic Redox Calculations: What Can and Cannot be Learned from Continuum Models, A. Warshel, A. Papazyan and I. Muegge, Int. J. Bioinorg. Chem. 2, 143-152 (1997).




  1. Electrostatic Basis of Enzyme Catalysis, G. Naray-Szabo, M. Fuxreiter and A. Warshel, in Computational Approaches to Biochemical Reactivity, eds. A. Warshel and G. Naray-Szabo, Kluwer Academic Publishers: p. 237-293 (1997).




  1. Consistent Calculations of pKa's of Ionizable Residues in Proteins: Semi-Microscopic and Macroscopic Approaches, Y. Y. Sham, Z. T. Chu and A. Warshel, J. Phys. Chem. B 101, 4458-4472 (1997).




  1. A Fundamental Assumption About OH- Attack in Phosphate Hydrolysis is Not Fully Justified, J. Flórian and A. Warshel, J. Am. Chem. Soc. 119, 5473-5474 (1997).




  1. Langevin Dipoles Model for Ab Initio Calculations of Chemical Processes in Solution: Parameterization and Application to Hydration Free Energies of Neutral and Ionic Solutes and Conformational Analysis in Aqueous Solution, J. Flórian and A. Warshel, J. Phys. Chem. 101, 5583-5595 (1997).




  1. On the Relationship Between the Dispersed Polaron and Spin-Boson Models, J.-K. Hwang and A. Warshel, Chem. Phys. Lett. 271, 223-225 (1997).




  1. The Reorganization Energy of Cytochrome c Revisited, I. Muegge, P. X. Qi, J. Wand, Z. T. Chu and A. Warshel, J. Phys. Chem. B 101, 825-836 (1997).




  1. Computer Simulations of the Action of Metalloenzymes, A. Warshel in Molecular Modeling and Dynamics of Bioinorganic Systems, eds. L. Banci and P. Comba, NATO: ASI Series, Kluwer Academic Publishers: p. 343-359 (1997).




  1. A Stringent Test of the Cavity Concept in Continuum Dielectrics, A. Papazyan and A. Warshel, J. Chem. Phys. 107, 7975-7978 (1997).




  1. Semiempirical and Ab Initio Modeling of Chemical Processes: From Aqueous Solution to Enzymes, R. P. Muller, J. Florian, A. Warshel in Biomolecular Structure and Dynamics, eds. G. Vergoten and T. Theophanides, NATO: ASI Series, Kluwer Academic Press: p. 47-77 (1997).




  1. Continuum and Dipole-Lattice Models of Solvation, A. Papazyan and A. Warshel, J. Phys. Chem. B 101, 11254-11264 (1997).




  1. A Fast Estimate of Electrostatic Group Contributions to the Free Energy of Protein-Inhibitor Binding, I. Muegge, H. Tao and A. Warshel, Protein Eng. 10, 1363-1372 (1997).




  1. Oscillations of the Energy Gap for the Initial Electron-Transfer Step in Bacterial Reaction Centers, W. W. Parson, Z. T. Chu and A. Warshel, Photosynth. Res. 55, 147-152, (1998).




  1. Origin of the Catalytic Power of Acetylcholinesterase: Computer Simulation Studies, M. Fuxreiter and A. Warshel, J. Am. Chem. Soc. 120, 183-194 (1998).




  1. Electrostatic Contributions to Protein-Protein Binding Affinities: Application to Rap/Raf Interaction, I. Muegge, T. Schweins and A. Warshel, Proteins 30, 407-423 (1998).




  1. Phosphate Ester Hydrolysis in Aqueous Solution: Associative Versus Dissociative Mechanisms, J. Flórian and A. Warshel, J. Phys. Chem. B 102, 719-734 (1998).




  1. Hybrid ab initio Quantum Mechanics/Molecular Mechanics Calculations of Free Energy Surfaces for Enzymatic Reactions: The Nucleophilic Attack in Subtilisin, J. Bentzien, R. P. Muller, J. Florián and A. Warshel, J. Phys. Chem. B 102, 2293-2301 (1998).




  1. Reorganization Energy of the Initial Electron-Transfer Step in Photosynthetic Bacterial Reaction Centers, W. W. Parson, Z. T. Chu, and A. Warshel, Biophys. J. 74, 182-191 (1998).




  1. Electrostatic Effects in Macromolecules: Fundamental Concepts and Practical Modeling, A. Warshel and A. Papazyan, Curr. Opin. in Struc. Biol. 8, 211-217 (1998).




  1. The Effect of Protein Relaxation on Charge-Charge Interactions and Dielectric Constants of Proteins, Y. Y. Sham, I. Muegge and A. Warshel, Biophys. J. 74, 1744-1753 (1998).




  1. Computer Simulations of Enzyme Catalysis. Finding Out What Has Been Optimized by Evolution, A. Warshel and J. Florián, Proc. Natl. Acad. Sci. USA 95, 5950-5955 (1998).




  1. Quantum Mechanical - Molecular Mechanical Approaches for Studying Chemical Reactions in Proteins and Solution, J. Bentzien, J. Florián, T. M. Glennon and A. Warshel in: Combined Quantum Mechanical & Molecular Mechanical Methods, ACS Symposium Series, 712, J. Gao and M. A. Thompson, eds., pp. 16-34 (1998).




  1. Conformational Flexibility of Phosphates, Phosphonate and Phosphorothiate Methyl Esters in Aqueous Solution, J. Florián and M. Strajbl and A. Warshel, J. Am. Chem. Soc. 120, 7959-7966 (1998).




  1. On the Reactivity of Phosphate Monoester Dianions in Aqueous Solution: Bronsted Linear Free-Energy Relationships Do Not Have a Unique Mechanistic Interpretation, J. Florián, J. Åqvist and A. Warshel, J. Am. Chem. Soc. 120, 11524-11525 (1998).




  1. Electrostatic Origin of the Catalytic Power of Enzymes and the Role of Preorganized Active Sites, A. Warshel, Mini Review, J. Biol. Chem. 273, 27035-27038 (1998).




  1. Energetics of the Catalytic Reaction of Ribonuclease A: A Computational Study of Alternative Mechanisms, T. M. Glennon and A. Warshel, J. Am. Chem. Soc. 120, 10234-10247 (1998).




  1. Energetics of Cation Radical Formation at the Proximal Active Site Tryptophan of Cytochrome c Peroxidase and Ascorbate Peroxidase, G. M. Jensen, S. W. Bunte, A. Warshel and D. B. Goodin, J. Phys. Chem. B 102, 8221-8228 (1998).




  1. The Surface Constraint All Atom Model Provides Size Independent Results in Calculations of Hydration Free Energies, Y. Y. Sham and A. Warshel, J. Chem. Phys. 109, 7940-7944 (1998).




  1. Free Energy Functions for Charge Separation in Wild-type and Mutant Bacterial Reaction Centers, W. W. Parson, Z. T. Chu, A. Warshel, in Photosynthesis: Mechanism and Effects. G. Garab, ed., (Kluwer Acad. Publ., Dordrecht) 2, 703-706 (1998).




  1. Effect of Solvent Discreteness on Solvation, A. Papazyan and A. Warshel, J. Phys. Chem. B 102, 5348-5357 (1998).




  1. Thermodynamic Parameters for Stacking and Hydrogen Bonding of Nucleic Acid Bases in Aqueous Solution. Ab Initio/Langevin Dipoles Study, J. Florián, J. Sponer and A. Warshel, J. Phys. Chem. B 103, 884-892 (1999).




  1. Mechanistic Alternatives in Phosphate Monoester Hydrolysis: What Conclusions Can be Drawn from Available Experimental Data?, J. Åqvist, K. Kolmodin, J. Florián and A. Warshel, Chem. Biol. 6, R71-R80 (1999).




  1. Catalytic Hydrolysis of Adenosine 2',3'-Cyclic Monophosphate by Cu(II) Terpyridine, L. A. Jenkins, J. K. Bashkin, J. D. Pennock, J. Florian and A. Warshel, Inorg. Chem. 38, 3215-3222 (1999).




  1. Role of Active Site Residues in the Glycosylase Step of T4 Endonuclease V. Computer Simulation Studies on Ionization States, M. Fuxreiter, A. Warshel and R. Osman, Biochemistry 38, 9577-9589 (1999).

  2. Simulating Proton Translocations in Proteins: Probing Proton Transfer Pathways in the Rhodobacter sphaeroides Reaction Center, Y. Y. Sham, I. Muegge and A. Warshel, Proteins 36, 484-500 (1999).




  1. Calculations of Hydration Entropies of Hydrophobic, Polar, and Ionic Solutes in the Framework of the Lnagevin Dipoles Solvation Model, J. Florian and A. Warshel, J. Phys. Chem. B 103, 10282-10288 (1999).




  1. Energetics and Dynamics of Transition States of Reactions in Enzymes and Solutions, A. Warshel and J. Bentzien, in "Transition State Modeling for Catlysis", ed. D. G. Truhlar and K. Morokuma, ACS Symposium Series 725, 489-499 (1999).




  1. Quantum Catalysis: The Modeling of Catalytic Transition States, M. B. Hall, P. Margl, G. Naray-Szabo, V. L. Schramm, D. G. Truhlar, R. A. van Santen, A. Warshel and J. L. Whitten, in "Transition State Modeling for Catalysis", ed. D. G. Truhlar and K. Morokuma, ACS Symposium Series 721, 2-17 (1999).




  1. Using Simplified Protein Representation as a Reference Potential for All-Atom Calculations of Folding Free Energy, Z.Z. Fan, J.-K. Hwang and A. Warshel, Theor. Chem. Acc. 103, 77-80 (1999).




  1. Quantum-Chemical Insights into Mechanisms of the Nonenzymatic Hydrolysis of Phosphate Monoesters, J. Florian and A. Warshel, Phosphorus Sulfur 144-146, 525-528 (1999).




  1. Microscopic Based Density Matrix Treatments of Electron-Transfer Reactions in Condensed Phases, C.F. Jen and A. Warshel, J. Phys. Chem. 103, 11378-11386 (1999).




  1. Computer Simulation of Biological Molecules, A. Warshel, Encyclopedia of Molecular Biology, Ed. T.E. Creighton, John Wiley & Sons, Inc., 555 (1999).




  1. Free Energy Calculations, A. Warshel, Encyclopedia of Molecular Biology, Ed. T. E. Creighton, John Wiley & Sons, Inc., 939 (1999).




  1. Molecular Mechanics, A. Warshel, Encyclopedia of Molecular Biology, Ed. T. E. Creighton, John Wiley & Sons, Inc., 1526 (1999).




  1. Potential Functions (Force Fields), A. Warshel, Encyclopedia of Molecular Biology Ed., T. E. Creighton, John Wiley & Sons, Inc., 1937 (1999).




  1. Monte Carlo Calculations, A. Warshel, Encyclopedia of Molecular Biology, Ed. T. E. Creighton, John Wiley & Sons, Inc., 1537 (1999).




  1. Neural Networks and Genetic Algorithms, A. Warshel, Encyclopedia of Molecular Biology, Ed. T. E. Creighton, John Wiley & Sons, Inc., 1589 (1999).




  1. Molecular Dynamics, A. Warshel, Encyclopedia of Molecular Biology, Ed. T. E. Creighton, John Wiley & Sons, Inc., 1527 (1999).




  1. Perspective on "The Energetics of Enzymatic Reactions”, A. Warshel, Proc. Natl. Acad. Sci. USA, 75, 5250 (1978)," Theor. Chem. Acc. 103, 337-339, (2000).




  1. What is the Relationship Between Dynamical Effects and Biological Functions? A. Warshel, in Simplicity and Complexity in Proteins and Nucleic Acids, eds. H. Frauenfelder, J. Deisenhofer, and P. G. Wolynes, Dahlem University Press, 199-211(2000).




  1. Group Report: How Does Complexity Lead to an Apparently Simple Function? K. Moffat, J.-P. Changeux, D. M. Crother, H. Grubmuller, G. U. Nienhaus, M. U. Palma, F. G. Parak, K. Schulten, and A. Warshel, in Simplicity and Complexity in Proteins and Nucleic Acids, eds. H. Frauenfelder, J. Deisenhofer, and P. G. Wolynes, Dahlem University Press, 255-280(2000).




  1. Ab Initio/LD Studies of Chemical Reactions in Solution: Reference Free-Energy Surfaces for Acylation Reactions Occurring in Serine and Cysteine Proteases, M. Strajbl, J. Florian and A. Warshel, Int. J. Quantum Chem. 77, 44-53(2000).




  1. Examining Methods for Calculations of Binding Free Energies: LRA, LIE, PDLD-LRA and PDLD/S-LRA Calculations of Ligands Binding to an HIV Protease, Y.Y. Sham, Z.T. Chu, H. Tao and A. Warshel, Proteins 39, 393-407 (2000).




  1. Ab Initio Evaluation of the Potential Surface for General Base Catalyzed Methanolysis of Formamide: A Reference Solution Reaction for Studies of Serine Proteases, M. Strajbl, J. Florian and A. Warshel, J. Am. Chem. Soc. 122, 5354-5366 (2000).




  1. An Effective Way of Modeling Chemical Catalysis: An Empirical Valence Bond Picture of the Role of Solvent and Catalyst in Alkylation Reactions, J. Villà, J. Bentzien, A. Gonzalez-Lafont, J.M. Lluch, J. Bertran and A. Warshel, J. Comput. Chem. 21, 607-625(2000).

  2. Computer Simulation Studies of the Catalytic Mechanism of Human Aldose Reductase, P. Varnai, A. Warshel, J. Am. Chem. Soc. 122, 3849-3860 (2000).




  1. Calculations of Activation Entropies of Chemical Reactions in Solution, M. Strajbl, Y. Sham, J. Villa, Z. T. Chu, A. Warshel, J. Phys. Chem. B 104, 4578-4584 (2000).




  1. How Does GAP Catalyze the GTPase Reaction of Ras? A Computer Simulation Study, T. M. Glennon, J.Villà and A. Warshel, Biochemistry 39, 9641-9651 (2000).




  1. How Important are Entropic Contributions to Enzyme Catalysis?, J. Villa, M. Strajbl, T. M. Glennon, Y. Y. Sham, Z. T. Chu and A. Warshel, Proc. Natl. Acad. Sci. USA 97, 11899-11904 (2000).




  1. Free-Energy Perturbation Calculations of DNA Destabilization by Base Substitutions: The Effect of Neutral Guanine-Thymine, Adenine-Cytosine and Adenine-Difluorotoluene Mismatches, J. Florian, M. F. Goodman and A. Warshel, J. Phys. Chem. B 104, 10092-10099 (2000).




  1. Remarkable Rate Enhancement of Orotidine 5’-Monophosphate Decarboxylase is Due to Transition-State Stabilization Rather than to Ground-State Destabilization, A. Warshel, M. Strajbl, J. Villa, J. Florian, Biochemistry 39, 14728-14738 (2000).




  1. Q-Chem 2.0: A High-Performance Ab Initio Electronic Structure Program Package: J. Kong, C. A. White, A. I. Krylov, D. Sherrill, R. D. Adamson, T. R. Furlani, M. S. Lee, A. M. Lee, S. R. Gwaltney, T.R. Adams, C. Ochsenfeld, A. T. B. Gilbert, G.S. Kedziora, V. A. Rassolov, D. R. Maurice, N. Nair, Y. Shao, N. A. Besley, P. E. Maslen, J. P. Dombroski, H. Daschel, W. Zhang, P. P. Korambath, J. Baker, E.F. C. Byrd, T. Van Voorhis, M. Oumi, S. Hirata, C-P. Hsu, N. Ishikawa, J. Florian, A. Warshel, B. G. Johnson, P. M. W. Gill, M. Head-Gordon and J. A. Pople, J. Comput. Chem. 21, 1532-1548 (2000).




  1. Constraining the Electron Densities in DFT Methods as an Effective Way for Ab Initio Studies of Metal-Catalyzed Reactions. G. Hong, M. Strajbel, T. Wesolowski and A. Warshel, J. Comput.Chem. 21, 1554-1561(2000).




  1. Comment on “A Fast and Simple Method to Calculate Protonation States in Proteins”, E. L. Mehler and A. Warshel, Proteins 40, 1-3 (2000).




  1. Dynamics of Biochemical and Biophysical Reactions: Insight from Computer Simulations, A. Warshel and W. W. Parson, Q. Rev. Biophys.34, 563-679 (2001).




  1. Circe Effect versus Enzyme Preorganization: What Can Be Learned from the Structure of the Most Proficient Enzyme?, A. Warshel, J. Florian, M. Strajbl, J. Villa, ChemBiochem 2, 109-111 (2001).




  1. Ab Initio Evaluation of the Free Energy Surfaces for the General Base/Acid Catalyzed Thiolysis of Formamide and the Hydrolysis of Methyl Thioformate: A Reference Solution Reaction for Studies of Cysteine Proteases, M. Strajbl, J. Florian, A. Warshel, J. Phys. Chem. B 105, 4471-4484 (2001).




  1. What are the Dielectric “Constants” of Proteins and How to Validate Electrostatic Models?, C. N. Schutz and A. Warshel, (Invited Review), Proteins 44, 400-417 (2001).




  1. Energetics and Dynamics of Enzymatic Reactions, J. Villa and A. Warshel, J. Phys. Chem. B 105, 7887-7907 (2001).




  1. Nature of the Surface Crossing Process in Bacteriorhodopsin: Computer Simulations of the Quantum Dynamics of the Primary Photochemical Event, A. Warshel and Z. T. Chu, J. Phys. Chem. B 105, 9857-9871 (2001).




  1. Simulations of Ion Current Realistic Models of Ion Channels: The KcsA Potassium Channel, A. Burykin, C. N. Schutz, J. Villa, and A. Warshel, Proteins 47, 265-280(2002).




  1. Modeling and Analyzing Biocatalysis, J. Villa and A. Warshel, Encyclopedia of Catalysis, Wiley (2002).




  1. Molecular Dynamics Simulations of Biological Reactions, A. Warshel, Accounts Chem. Res. 35, 385-395 (2002).




  1. Theoretical Investigation of the Binding Free Energies and Key Substrate-Recognition Components of DNA Polymerase β Fidelity, J. Florian, M. F. Goodman, and A. Warshel, J. Phys. Chem. B 106, 5739-5753 (2002).




  1. Molecular Dynamics Free Energy Simulations of the Binding Contribution to the Fidelity of DNA Polymerase T7, J. Florian, A. Warshel, and M. F. Goodman, J. Phys. Chem. B 106, 5754-5760 (2002).




  1. How Much Do Enzymes Really Gain by Restraining Their Reacting Fragments?, A. Shurki, M. Strajbl, J. Villa, and A. Warshel, J. Am. Chem. Soc. 124, 4097-4107 (2002).




  1. Ab-initio QM/MM Simulation with Proper Sampling: “First Principle” Calculations of the Free Energy of the Auto-dissociation of Water in Aqueous Solution, M. Strajbl, G. Hong, and A. Warshel, J. Phys. Chem. B 106,13333-13343 (2002).




  1. Computer Simulations of Enzyme Catalysis: Methods, Progress and Insights, A. Warshel, Annual Review of Biophysics and Biomolecular Structure 32, 425-443 (2003).




  1. Frozen Density Functional Free Energy Simulations of Redox Proteins: Computational Studies of the Reduction Potential of Plastocyanin and Rusticyanin, M.H. Olsson, G. Hong and A. Warshel, J. Am. Chem. Soc. 125, 5025-5039 (2003).




  1. On the Generation of Catalytic Antibodies by Transition State Analogues, M. Barbany, H. Gutierrez-de-Teran, F. Sanz, J. Villa and A. Warshel, ChemBiochem 4, 277-285 (2003).




  1. Computer Simulation Studies of the Fidelity of DNA Polymerases, J. Florian, M. Goodman, and A. Warshel, Biopolymers 68, 286-299 (2003).




  1. Structure/Function Correlations of Enzymes using MM, QM/MM and Related Approaches; Methods, Concepts, Pitfalls and Current Progress, A. Shurki and A. Warshel., Advances in Protein Chemistry 66, 249-313 (2003).




  1. Computer Simulation of the Chemical Catalysis of DNA Polymerases: Discriminating Between Alternative Nucleotide Insertion Mechanisms for T7 DNA Polymerase, J. Florian, M. F. Goodman and A. Warshel, J. Am. Chem. Soc. 125, 8163-8177 (2003).




  1. Apparent NAC Effect in Chorismate Mutase Reflects Electrostatic Transition State Stabilization, M. Strajbl, A. Shurki, M. Kato and A. Warshel, J. Am. Chem. Soc. 125, 10228-10237 (2003).




  1. Comment on “Effect of Active Site Mutation Phe93Trp in the Horse Liver Alcohol Dehydrogenase Enzyme on Catalysis: A Molecular Dynamics Study”, A. Warshel and J. Villà-Freixa, J. Phys. Chem. B 107, 12370-12371 (2003).

  2. Exploring the Origin of the Ion Selectivity of the KcsA Potassium Channel, A. Burykin, M. Kato and A. Warshel, Proteins 52, 412-426 (2003).




  1. What Really Prevents Proton Transport Through Aquaporin? Charge Self-Energy vs. Proton Wire Proposals, A. Burykin and A. Warshel, Biophys. J. 85, 3696-3706(2003).




  1. Converting Conformational Changes to Electrostatic Energy in Molecular Motors: The Energetics of ATP Synthase m, M. Strajbl, A. Shurki and A. Warshel, Proc. Natl. Acad. Sci. USA 100, 14834-14839 (2003).




  1. A Density Matrix Model of Photosynthetic Electron Transfer with Microscopically Based Estimated Vibrational Relaxation Times, W. W. Parson and A. Warshel, Chem. Phys. 296, 201-216 (2004).




  1. Simulating Large Nuclear Quantum Mechanical Corrections in Hydrogen Atom Transfer Reactions in Metalloenzymes, M. H. M. Olssen, P. E. M Siegbahn and A. Warshel, J. Biol. Inorg. Chem. 9, 96-99 (2004).




  1. Analyzing Linear Free Energy Relationship for Proton Translocations in Enzymes; Carbonic Anhydrase Revisited, C. N. Schutz and A. Warshel, J. Phys. Chem. B 108, 2066-2075 (2004).




  1. Electrostatic Basis for Bioenergetics. Shurki, M. Strajbl, C. N. Schutz and A. Warshel. Method Enzymol. 380, 52-84 (2004).




  1. Why does the Ras Switch “Break” By Oncogenic Mutations?, A. Shurki, A. Warshel, Proteins 55, 1-10 (2004).




  1. Simulations of the Large Kinetic Isotope Effect and the Temperature Dependence of the Hydrogen Transfer in Lipoxygenase, M. H. M. Olsson, P. E. M Siegbahn and A. Warshel, J. Am. Chem. Soc. 126, 2820-2828 (2004).




  1. The Low Barrier Hydrogen Bond (LBHB) Proposal Revisited: The Case of the Asp…His Pair in Serine Proteases, C. N. Schutz and A. Warshel, Proteins 55, 711-723 (2004).




  1. Dependence of Photosynthetic Electron-Transfer Kinetics on Temperature and Energy in a Density-Matrix Model, W. W. Parson and A. Warshe, J. Phys. Chem. B. 108, 10474-10483 (2004).




  1. On the Origin of the Electrostatic Barrier for Proton Transport in Aquaporin, A. Burykin and A. Warshel, FEBS Lett. 570, 41-46 (2004).




  1. Solute Solvent Dynamics and Energetics in Enzyme Catalysis: The SN2 Reaction of Dehalogenase as a General Benchmark, M. H. M. Olsson and A. Warshel, J. Am. Chem. Soc. 126, 15167-15179 (2004).




  1. Studies of Proton Translocations in Biological Systems: Simulating Proton Transport in Carbonic Anhydrase by EVB Based Models, S. Braun-Sand, M. Strajbl, and A. Warshel. Biophys. J. 87, 2221-2239 (2004).




  1. The Empirical Valence Bond, A. Warshel and J. Florian, The Encyclopedia of Computational Chemistry (2004).




  1. Realistic Simulations of Proton Transport Along the Gramicidin Channel: Demonstrating the Importance of Solvation Effects, S. Braun-Sand, A. Burykin, and A. Warshel, J. Phys. Chem. B. 109, 583-592 (2005).

  2. Inverting the Selectivity of Aquaporin 6: Gating versus Direct Electrostatic Interaction, A. Warshel, Proc. Natl. Acad. Sci. USA 102, 1813-1814 (2005).




  1. Electrostatics of Proteins: Principles, Models and Applications S. Braun-Sand and A. Warshel in Protein Folding Handbook. Part I. Edited by J. Buchner and T. Kiefhaber 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim, p. 163-200 (2005).




  1. Simulating Redox Coupled Proton Transfer in Cytochrome c Oxidase; Looking for the Proton Bottleneck, M. H. M. Olsson, P. K. Sharma and A. Warshel, FEBS Lett. 579, 2026-2034 (2005).




  1. Computer Simulations of Protein Functions: Searching for the Molecular Origin of the Replication Fidelity of DNA Polymerases. J. Florián, M. F. Goodman and A. Warshel, Proc. Natl. Acad. Sci. USA 102, 6819-6824 (2005).




  1. What are the Roles of Substrate-Assisted Catalysis and Proximity Effects in Peptide Bond Formation by the Ribosome?, P. K. Sharma, Y. Xiang, M. Kato, and A. Warshel, Biochemistry 44, 11307-11314 (2005).




  1. On Possible Pitfalls in Ab Initio Quantum Mechanics/Molecular Mechanics Minimization Approaches for Studies of Enzymatic Reactions, M. Klahn, S. Braun-Sand, E. Rosta, and A. Warshel, J. Phys. Chem. B 109,15645-15650 (2005)




  1. Through the Channel and Around the Channel: Validating and Comparing Microscopic Approaches for the Evaluation of Free Energy Profiles for Ion Penetration through Ion Channels, M. Kato and A. Warshel. J. Phys. Chem. B. 109, 19516-19522 (2005)




  1. Computer Modeling of Enzyme Catalysis and its Relationship to Concepts in Physical Organic Chemistry, S. Braun-Sand, M.H.M. Olsson, A. Warshel in Advances in Physical Organic Chemistry, ed. J.P. Richard,Vol. 40, 201-245 (2005).




  1. Computer Simulations of Isotope Effects in Enzyme Catalysis, A. Warshel, M. H. M. Olsson, and J. Villà-Freixa, in Isotope Effects In Chemistry and Biology, ed. A. Kohen and H-H Limbach, CRC press, pp. 621-644 (2005).




  1. Towards Accurate Ab Initio QM/MM Calculations of Free-Energy Profiles of Enzymatic Reactions; E. Rosta, M. Klahn, and A Warshel, J. Phys. Chem. B 110, 2934-2941 (2006).




  1. Dynamical Contributions to Enzyme Catalysis: Critical Tests of a Popular Hypothesis; M. H. M. Olsson, W. W. Parson and A. Warshel, Chem. Rev. 106, 1737-1756 (2006).




  1. Using a Charging Coordinate in Studies of Ionization Induced Partial Unfolding; M. Kato and A Warshel, J. Phys. Chem. B 110, 11566-11570 (2006).




  1. Monte Carlo Simulations of Proton Pumps: On the Working Principles of the Biological Valve that Controls Proton Pumping in Cytochrome c Oxidase; M. H. M. Olsson and A. Warshel, Proc. Natl. Acad. Sci. USA 103, 6500-6505 (2006).




  1. Membranes Assembled from Narrow Carbon Nanotubes Block Proton Transport and Can Form Effective Nano Filtration Devices; A Burykin and A Warshel, Journal of Computational Theoretical Nanoscience, 3, 237-242 (2006).




  1. Transition State Theory Can be Used in Studies of Enzyme Catalysis: Lessons from Simulations of Tunnelling and Dynamical Effects in Lipoxygenase and Other Systems; M. H. M. Olsson, J. Mavri and A. Warshel, Philos. T. R. Soc. London B – Biol. Sci. 361, 1417-1432 (2006).




  1. The Barrier for Proton Transport in Aquaporins as a Challenge for Electrostatic Models: The Role of Protein Relaxation in Mutational Calculations M. Kato, A. V. Pisliakov, and A. Warshel. Proteins 64, 829-844 (2006).




  1. Simulating the Effect of DNA Polymerase Mutations on Transition-State Energetics and Fidelity: Evaluating Amino Acid Group Contribution and Allosteric Coupling for Ionized Residues in Human Pol beta; Y. Xiang, P. Oelschlaeger, J. Florian, M. F. Goodman, A. Warshel, Biochemistry 45, 7036-7048 (2006)




  1. Electrostatic Basis for Enzyme Catalysis; A. Warshel, P. K. Sharma, M. Kato, Y. Xiang, H. Liu, and M. H. M. Olsson, Chem. Rev. 106, 3210-3235 (2006).




  1. Modeling Electrostatic Effects in Proteins; A. Warshel, P. K. Sharma, M. Kato and W. W. Parson, BBA-Proteins Proteom. 1764, 1647-1676 (2006).




  1. Using the Constrained DFT Approach in Generating Diabatic Surfaces and Off Diagonal Empirical Valence Bond Terms for Modeling Reactions in Condensed Phases, G. Hong, E. Rosta and A. Warshel, J. Phys. Chem. B.110, 19570-19574 (2006).




  1. On the Mechanism of Hydrolysis of Phosphate Monoesters Dianions in Solutions and Proteins; M. Klahn, E. Rosta and A. Warshel, J. Am. Chem. Soc. 128, 15310-15323 (2006).




  1. Modifying the beta, gamma Leaving-Group Bridging Oxygen Alters Nucleotide Incorporation Efficiency, Fidelity, and the Catalytic Mechanism of DNA Polymerase beta; C. Sucato, T. G. Upton, B. A. Kashemirov, V. K. Batra, V. Martinek, Y. Xiang, W. A. Beard, L. C. Petersen, S. H. Wilson, C. E. McKenna, J. Florian, A. Warshel, M. F. Goodman, Biochemistry 46, 461-471 (2007).




  1. Magnesium-Cationic Dummy Atom Molecules Enhanced Representation of DNA Polymerase β in Molecular Dynamics Simulations: Improved Accuracy in Studies of Structural Features and Mutational Effects; P. Oelschlaeger, M. Klahn, W. A. Beard, S. H. Wilson and Arieh Warshel, J. Mol. Biol. 366, 687-701 (2007).




  1. DNA Polymerase β Catalytic Efficiency Mirrors the Asn279–dCTP H-Bonding Strength, V. Martınek, U. Bren, M. F. Goodman, A. Warshel and J. Florian, FEBS Lett. 581,775-780 (2007).




  1. Exploring Pathways and Barriers for Coupled ET/PT in Cytochrome c Oxidase: A General Framework for Examining Energetics and Mechanistic Alternatives. M. H. M. Olsson, P. E. M. Siegbahn, M. R. A. Blomberg, and A. Warshel, BBA-Bioenergetics 1767, 244-260 (2007).




  1. Electrostatic Contributions to Binding of Transition State Analogues Can Be Very Different from the Corresponding Contributions to Catalysis: Phenolates Binding to the Oxyanion Hole of Ketosteroid Isomerase, A. Warshel, P. K. Sharma, Z. T. Chu and J. Aqvist, Biochemistry 46, 1466-1476 (2007).




  1. Electrostatic Contributions to Protein Stability and Folding Energy; M. Roca, B. Messer and A. Warshel, FEBS Lett. 581, 2065-2071(2007).




  1. The Catalytic Effect of Dihydrofolate Reductase and its Mutants is Determined by Reorganization Energies, H. Liu and A. Warshel, Biochemistry 46, 6011-6025 (2007).




  1. Origin of the Temperature Dependence of Isotope Effects in Enzymatic Reactions: The Case of Dihydrofolate Reductase, H. Liu and A. Warshel, J. Phys. Chem. B 111, 7852-7861 (2007).




  1. A New Paradigm for Electrostatic Catalysis of Radical Reactions in Vitamin B-12 Enzymes, P. K. Sharma, Z. T. Chu, M. H. M. Olsson and A. Warshel, Proc. Natl. Acad. Sci. USA 104, 9661-9666 (2007).




  1. Polarizable Force Fields: History, Test Cases, and Prospects, A. Warshel, M. Kato, and A.V. Pisliakov, J. Chem. Theory Comput. 3, 2034-2045 (2007).




  1. On the Relationship Between Thermal Stability and Catalytic Power of Enzymes, M. Roca, H. Liu, B. Messer, and A. Warshel, Biochemistry 46, 15076-15088 (2007)




  1. Computer simulations of Proton transfer in proteins and Solutions, S, Braun-Sand, M. H. M. Olsson, J. Mavri and A. Warshel in Hydrogen –Transfer Reactions. Ed J. T. Hynes, J. P. Klinmann, H. H. Limbach and R. L. Schowen WILEY-VCH Verlag GmbH&Co KGaA, Weinheim, 1171- 1205 (2007)




  1. Challenges and Progresses in Calculations of Binding Free Energies – What Does it Take to Quantify Electrostatic Contributions to Protein–Ligand Interactions? M. Kato, S. Braun-Sand and A. Warshel, in Computational and Structural Approaches to Drug Discovery, Ed by R. M. Stroud and J. Finer–Moore, RSC Publishing, 268-292 (2008).




  1. Prediction of Drug Resistance Mutation of HIV Protease, H. Ishikita and A. Warshel, Angew. Chem. Int. Ed., 47, 697-700 (2008).




  1. Exploring the Role of Large Conformational Changes in the Fidelity of DNA Polymerase β; Y. Xiang, M. F. Goodman, W. A. Beard, S. H. Wilson and A. Warshel, Proteins 70, 231-247 (2008).




  1. DNA Polymerase β Fidelity: Halomethylene-Modified Leaving Groups in Pre-Steady-State Kinetic Analysis Reveal Differences at the Chemical Transition State, C. A. Sucato, T. G. Upton, B. A. Kashemirov, J. Osuna, K. Oertell, W. A. Beard, .S. H. Wilson, J. Florian, A. Warshel, C. E. McKenna, and M. F. Goodman, Biochemistry 47, 870-879 (2008)




  1. Calculations of Electrostatic Energies in Proteins: Using Microscopic, Semimicroscopic and Macroscopic Models and Free Energy Perturbation Approaches, W. W. Parson and A. Warshel, in Biophysical Techniques in Photosystem II, Ed. J. Aartmas and J. Matysik, Springer, The Netherlands, 401-420 (2008).




  1. Mechanism of Charge Separation in Purple Bacterial Reaction Centers, W.W. Parson and A. Warshel, in the Purple Photosynthetic Bacteria ed. N. Hunter, F. Daldal, M. C. Thurnauer and J.T. Beatty. Springer (2008).




  1. Quantifying Free Energy Profiles of Proton Transfer Reactions in Solution and in Proteins by Using a Diabatic FDFT Mapping, Y. Xiang and A. Warshel, J. Phys. Chem. B 112, 1007-1015 (2008).




  1. Simulation of Tunneling in Enzyme Catalysis by Combining a Biased Propagation Approach and the Quantum Classical Path Method: Application to Lipoxygenase, J. Mavri, H. Liu, M.H.M. Olsson and A. Warshel, J. Phys. Chem. B 112, 5950-5954 (2008).




  1. On the Interpretation of the Observed Linear Free Energy Relationship in Phosphate Hydrolysis: A Thorough Computational Study of Phosphate Diester Hydrolysis in Solution, E. Rosta, S. C. L. Kamerlin and A. Warshel, Biochemistry 47, 3725–3735 (2008).




  1. The Energetics of the Primary Proton Transfer in Bacteriorhodopsin Revisited: It is a Sequential Light-Induced Charge Separation After All, S. Braun-Sand, P. K. Sharma, Z. T. Chu, A. V. Pisliakov, A. Warshel, BBA-Bioenergetics 1777, 441–452 (2008).




  1. Electrostatic Basis for the Unidirectionality of the Primary Proton Transfer in Cytochrome Oxidase, A.V. Pisliakov, P. K. Sharma, Z. T. Chu, M. Haranczyk, and A. Warshel, Proc. Natl. Acad. Sci. USA 105, 7726-7731 (2008).




  1. Associative Versus Dissociative Mechanisms of Phosphate Monoester Hydrolysis: On the Interpretation of Activation Entropies, S. C. L. Kamerlin, J. Florian, and A. Warshel, ChemPhysChem 9, 1767-1773 (2008).




  1. Accelerating QM/MM Free Energy Calculations: Representing the Surroundings by an Updated Mean Charge Distribution, E. Rosta, M, Haranczyk, Z. T. Chu and A. Warshel, J. Phys. Chem. B 112, 5680-5692 (2008).




  1. Solvation Free Energies of Molecules. The Most Stable Anionic Tautomers of Uracil M. Haranczyk, M. Gutowski and A. Warshel, Phys. Chem. Chem. Phys. 10, 4442–4448 (2008).




  1. On the Relationship Between Folding and Chemical Landscapes in Enzyme Catalysis, M. Roca, B. Messer, D. Hilvert and A. Warshel, Proc. Natl. Acad. Sci. USA 105, 13877-13882 (2008)




  1. Dineopentyl Phosphate Hydrolysis: Evidence for Stepwise Water Attack, S. C. L. Kamerlin, N. H. Williams and A. Warshel, J. Org. Chem. FEATURE ARTICLE 73, 6960-6969 (2008).




  1. Progresses in Ab Initio QM/MM Free Energy Simulations of Electrostatic Energies in Proteins: Accelerated QM/MM Studies of pKa, Redox Reactions and Solvation Free Energies, S. C. L. Kamerlin, M. Haranczyk and A. Warshel, J. Phys. Chem. B, Centennial Feature Article 113, 1253-1272 (2009).




  1. Tunneling Does Not Contribute Significantly to Enzyme Catalysis, But Studying Temperature Dependence of Isotope Effects is Useful, H. Liu and A. Warshel, RSC Biomolecular Sciences, Quantum Tunneling in Enzyme-Catalyzed Reactions, Ed. by R. K. Allemann and N. S. Scrutton, Royal Society of Chemistry, 242-267 (2009).




  1. Toward Accurate Screening in Computer-Aided Enzyme Design, M. Roca, A. Vardi-Kilshtain and A. Warshel, Biochemistry 48, 3046-3056 (2009).




  1. The Empirical Valence Bond as an Effective Strategy for Computer-Aided Enzyme Design, A. Vardi-Kilshtain, M. Roca and A. Warshel, Biotechnol. J. 4, 495-500 (2009).




  1. Toward Accurate Microscopic Calculation of Solvation Entropies: Extending the Restraint Release Approach to Studies of Solvation Effects, N. Singh and A. Warshel, J. Phys. Chem. B 113, 7372-7382 (2009).




  1. Simulating the Electrostatic Guidance of the Vectorial Translocations in Hexameric Helicases and Translocases, H. Liu, Y. Shi, X. S. Chen, and A. Warshel, Proc. Natl. Acad. Sci. USA 106, 7449-7454 (2009).




  1. Are Mixed Explicit/Implicit Solvation Models Reliable for Studying Phosphate Hydrolysis? A Comparative Study of Continuum, Explicit and Mixed Solvation Models, S. C. L. Kamerlin, M. Haranczyk and A. Warshel, ChemPhysChem 10, 1125-1134 (2009).




  1. A Computational Study of the Hydrolysis of dGTP Analogues with Halomethylene-Modified Leaving Groups in Solution: Implications for the Mechanism of DNA Polymerases, S. C. L. Kamerlin, C. E. McKenna, M. F. Goodman and A. Warshel, Biochemistry 48, 5963-5971 (2009).




  1. On Unjustifiably Misrepresenting the EVB Approach While Simultaneously Adopting It, S. C. L. Kamerlin, J Cao, E. Rosta and A Warshel, J. Phys. Chem. B 113, 10905-10915 (2009).




  1. Enzyme Millisecond Conformational Dynamics Do Not Catalyze the Chemical Step, A. V. Pisliakov J. Cao, S. C. L. Kamerlin and A. Warshel, Proc. Natl. Acad. Sci. USA 106, 17359-17364 (2009).




  1. On the Energetics of ATP Hydrolysis in Solution, S. C. L. Kamerlin and A. Warshel, J. Phys. Chem. B 113, 15692-15698 (2009).




  1. On the Origin of the Catalytic Power of Carboxypeptidase A and Other Metalloenzymes, A. V. Kilshtain and A. Warshel, Proteins 77, 536-550 (2009).




  1. Effective Approach for Calculations of Absolute Stability of Proteins Using Focused Dielectric Constants, S. Vicatos, M. Roca and A. Warshel, Proteins 77, 670-684 (2009).




  1. A Binding Free Energy Decomposition Approach for Accurate Calculations of the Fidelity of DNA Polymerases, R. Rucker, P. Oelschlaeger and A. Warshel, Proteins 78, 671-680 (2010).




  1. Multiscale Simulations of Protein Landscapes: Using Coarse-Grained Models as Reference Potentials to Full Explicit Models, B. M. Messer, M. Roca, Z. T. Chu, S. Vicatos, A. V. Kilshtain and A. Warshel, Proteins 78, 1212-1227 (2010).




  1. At the Dawn of the 21st Century: Is dynamics the Missing Link for Understanding Enzyme Catalysis? S. C. L. Kamerlin and A. Warshel, Proteins (INVITED REVIEW) 78, 1339-1375 (2010).

  2. Absolute Binding Free Energy Calculations: On the Accuracy of Computational Scoring of Protein-Ligand Interactions, N. Singh and A. Warshel, Proteins 78, 1705-1723 (2010).

  3. A Comprehensive Examination of the Contributions to the Binding Entropy of Protein-Ligand Complexes, N. Singh and A. Warshel, Proteins 78, 1724-1735 (2010).




  1. Ketosteroid Isomerase Provides Further Support for the Idea that Enzymes Work by

Electrostatic Preorganization, S. C.L. Kamerlin, P. K. Sharma, Z. T. Chu and A. Warshel, Proc. Natl. Acad. Sci. USA 107, 4075-4080 (2010)


  1. Reply to Karplus: Conformational Dynamics Have no Role in The Chemical Step, S. C. L. Kamerlin and A. Warshel, Proc. Natl. Acad. Sci. USA 107, E72 (2010).




  1. Examining the Case for the Effect of Barrier Compression on Tunneling, Vibrationally Enhanced Catalysis, Catalytic Entropy and Related Issues (Review), S.C.L. Kamerlin, J. Mavri and A. Warshel, FEBS Lett. 584, 2759-2766 (2010).




  1. Exploring Challenges in Rational Enzyme Design by Simulating the Catalysis in Artificial Kemp Eliminase, M. P. Frushicheva, J. Cao, Z. T. Chu and A. Warshel, Proc. Natl. Acad. Sci. USA 107, 16869-16874 (2010).




  1. An Analysis of All the Relevant Facts and Arguments Indicates that Enzyme Catalysis Does Not Involve Large Contributions from Nuclear Tunneling, S. C. L. Kamerlin and A. Warshel, J. Phys. Org. Chem. 23, 677-684 (2010).




  1. Renormalizing SMD: The Renormalization Approach and Its Use in Long Time Simulations and Accelerated PMF Calculations of Macromolecules, A. Dryga and A. Warshel, J. Phys. Chem. B 114, 12720-12728 (2010).




  1. On the Energetics of Translocon Assisted Insertion of Charged Transmembrane Helices into Membranes, A. Rychkova, S. Vicatos, and A. Warshel, Proc. Natl. Acad. Sci. USA 107, 17598-17603 (2010).




  1. On Catalytic Preorganization in Oxyanion Holes: Highlighting the Problems with the Gas Phase Modeling of Oxyanion Holes and Illustrating the Need for Complete Enzyme Models, S. C. L. Kamerlin, Z. T. Chu and A. Warshel, J. Org. Chem. 75, 6391-6401 (2010).




  1. The EVB as a Quantitative Tool for Formulating Simulations and Analyzing Biological and Chemical Reactions, S. C. L. Kamerlin and A. Warshel, Faraday Discuss. 145, 71-106 (2010).




  1. Phosphate Ester Analogues as Probes for Understanding Enzyme Catalyzed Phosphoryl Transfer, A. Alkherraz, S. C. L. Kamerlin, G. Feng, Q. I. Sheikh, A. Warshel and N. H. Williams, Faraday Discuss. 145, 281-299 (2010).




  1. Coarse-Grained (Multiscale) Simulations in Studies of Biophysical and Chemical Systems, S. C. L. Kamerlin, S. Vicatos, A. Dryga and A. Warshel, Annu. Rev. Phys. Chem. 62, 41-64 (2011).




  1. Exploration of the Cytochrome c Oxidase Pathway Puzzle and Examination of the Origin of Elusive Mutational Effects, S. Chakrabarty, I. Namslauer, P. Brzezinski and A. Warshel, BBA-Bioenergetics 1807, 413-426 (2011).




  1. The Empirical Valence Bond Model: Theory and Applications S. C. L. Kamerlin and A. Warshel, Wiley Interdisciplinary Reviews: Computational Molecular Sciences 1, 30-45 (2011).




  1. Challenges and Advances in Validating Enzyme Design Proposals: The Case of the Kemp Eliminase Catalysis, M. P. Frushicheva, J. Cao and A. Warshel, Biochemistry 50, 3849-3858 (2011).




  1. Proton-Transport Mechanisms in Cytochrome c Oxidase Revealed by Studies of Kinetic Isotope Effects, A.L. Johansson, S. Chakrabarty, C. B. Siöberg, M. Högbom, A. Warshel and P. Brzezinski, BBA-Bioenergetics 1807, 1083-1094 (2011).




  1. Converting Structural Information into an Allosteric-Energy-Based Picture for Elongation Factor to Activation by the Ribosome, A. J. Adamczyk and A. Warshel, Proc. Natl. Acad. Sci. USA 108, 9827-9832 (2011).




  1. Paradynamics: An Effective and Reliable Model for Ab Initio QM/MM Free-Energy Calculations and Related Tasks, N. V. Plotnikov, S. C. L. Kamerlin and A. Warshel, J. Phys. Chem. B 115, 7950-7962 (2011).




  1. Multiscale Modeling of Biological Functions, S. C. L. Kamerlin and A. Warshel, Phys. Chem. Chem. Phys. 13, 10401-10411 (2011).




  1. Catalysis by Dihydrofolate Reductase and Other Enzymes Arises from Electrostatic Preorganization, Not Conformational Motions, A. J. Adamczyk, J. Cao, S. C. L. Kamerlin and A. Warshel, Proc. Natl. Acad. Sci. USA 108, 14115-14120 (2011).




  1. Prechemistry versus Preorganization in DNA Replication Fidelity, R. B. Prasad and A. Warshel. Proteins 79, 2900-2919, (2011).




  1. Electrostatic Origin of the Mechanochemical Rotary Mechanism and The Catalytic Dwell of F1-ATPase, S. Mukherjee and A. Warshel, Proc. Natl. Acad. Sci. USA 108, 20550-20555 (2011).




  1. Simulating Electrostatic Energies in Proteins: Perspectives and Some Recent Studies of pK(a)s, Redox, and Other Crucial Functional Properties, A. Warshel and A. Dryga, Proteins 79, 3469-3484 (2011).




  1. Coarse Grained Model for Exploring Voltage Dependent Ion Channels, A. Dryga, S. Chakrabarty, S. Vicatos, A. Warshel, BBA-Biomembranes 1818, 303-317 (2012).




  1. Realistic Simulation of the Activation of Voltage-Gated Ion Channels, A. Dryga, S. Chakrabarty, S. Vicatos and A. Warshel, Proc. Natl. Acad. Sci. USA 109, 3335

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