Arieh Warshel
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Chemist, biochemist and biophysicist
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Arieh Warshelbiology Degrees
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Arieh Warshelphysics Degrees
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Biology Physics
Arieh Warshel's Degrees
- PhD Chemistry Weizmann Institute of Science
- Masters Chemistry Weizmann Institute of Science
- Bachelors Chemistry Technion – Israel Institute of Technology
Why Is Arieh Warshel Influential?
(Suggest an Edit or Addition)According to Wikipedia, Arieh Warshel is an Israeli-American biochemist and biophysicist. He is a pioneer in computational studies on functional properties of biological molecules, Distinguished Professor of Chemistry and Biochemistry, and holds the Dana and David Dornsife Chair in Chemistry at the University of Southern California. He received the 2013 Nobel Prize in Chemistry, together with Michael Levitt and Martin Karplus for "the development of multiscale models for complex chemical systems".
Arieh Warshel's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. (1976) (3403)
- Advances in molecular quantum chemistry contained in the Q-Chem 4 program package (2014) (2204)
- Advances in methods and algorithms in a modern quantum chemistry program package. (2006) (2045)
- Electrostatic basis for enzyme catalysis. (2006) (963)
- Computer Modeling of Chemical Reactions in Enzymes and Solutions (1991) (938)
- Computer simulation of protein folding (1975) (930)
- Calculations of electrostatic interactions in biological systems and in solutions (1984) (803)
- What are the dielectric “constants” of proteins and how to validate electrostatic models? (2001) (802)
- An empirical valence bond approach for comparing reactions in solutions and in enzymes (1980) (709)
- Calculation of ground and excited state potential surfaces of conjugated molecules. I. Formulation and parametrization (1972) (618)
- Frozen density functional approach for ab initio calculations of solvated molecules (1993) (610)
- Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches (1993) (608)
- Consistent Force Field for Calculations of Conformations, Vibrational Spectra, and Enthalpies of Cycloalkane and n‐Alkane Molecules (1968) (578)
- Dynamics of reactions in polar solvents. Semiclassical trajectory studies of electron-transfer and proton-transfer reactions (1982) (486)
- Modeling electrostatic effects in proteins. (2006) (455)
- Electrostatic Origin of the Catalytic Power of Enzymes and the Role of Preorganized Active Sites* (1998) (423)
- At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis? (2010) (413)
- Bicycle-pedal model for the first step in the vision process (1976) (403)
- Computer simulations of enzyme catalysis: methods, progress, and insights. (2003) (393)
- Q‐Chem 2.0: a high‐performance ab initio electronic structure program package (2000) (388)
- A surface constrained all‐atom solvent model for effective simulations of polar solutions (1989) (366)
- How do serine proteases really work? (1989) (366)
- Energetics of enzyme catalysis. (1978) (364)
- A local reaction field method for fast evaluation of long‐range electrostatic interactions in molecular simulations (1992) (349)
- Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs (1993) (344)
- Electrostatic energy and macromolecular function. (1991) (339)
- Investigation of the free energy functions for electron transfer reactions (1990) (317)
- Consistent Calculations of pKa's of Ionizable Residues in Proteins: Semi-microscopic and Microscopic Approaches (1997) (303)
- Consistent Force Field Calculations. II. Crystal Structures, Sublimation Energies, Molecular and Lattice Vibrations, Molecular Conformations, and Enthalpies of Alkanes (1970) (298)
- Polarizable Force Fields: History, Test Cases, and Prospects. (2007) (283)
- Calculations of enzymatic reactions: calculations of pKa, proton transfer reactions, and general acid catalysis reactions in enzymes. (1981) (275)
- Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603. (1992) (272)
- Calculations of chemical processes in solutions (1979) (271)
- Progress 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. (2009) (261)
- Energetics and Dynamics of Enzymatic Reactions (2001) (259)
- Electrostatic basis of structure-function correlation in proteins (1981) (256)
- Electrostatic effects in macromolecules: fundamental concepts and practical modeling. (1998) (245)
- Microscopic examination of free-energy relationships for electron transfer in polar solvents (1987) (238)
- Microscopic models for quantum mechanical calculations of chemical processes in solutions: LD/AMPAC and SCAAS/AMPAC calculations of solvation energies (1992) (238)
- Substrate-assisted catalysis as a mechanism for GTP hydrolysis of p21ras and other GTP-binding proteins (1995) (234)
- Why nature really chose phosphate (2013) (232)
- Simulation of free energy relationships and dynamics of SN2 reactions in aqueous solution (1988) (224)
- Protein Control of Redox Potentials of Iron−Sulfur Proteins (1996) (222)
- Calculations of electrostatic energies in proteins. The energetics of ionized groups in bovine pancreatic trypsin inhibitor. (1985) (218)
- On low-barrier hydrogen bonds and enzyme catalysis. (1995) (217)
- Dynamical contributions to enzyme catalysis: critical tests of a popular hypothesis. (2006) (211)
- Enzyme millisecond conformational dynamics do not catalyze the chemical step (2009) (205)
- Electrostatic control of charge separation in bacterial photosynthesis. (1990) (203)
- Dynamics of biochemical and biophysical reactions: insight from computer simulations (2001) (203)
- Macroscopic models for studies of electrostatic interactions in proteins: limitations and applicability. (1984) (199)
- Microscopic simulations of macroscopic dielectric constants of solvated proteins (1991) (197)
- Free energy of charges in solvated proteins: microscopic calculations using a reversible charging process. (1986) (196)
- Frozen density functional free energy simulations of redox proteins: computational studies of the reduction potential of plastocyanin and rusticyanin. (2003) (189)
- Control of the redox potential of cytochrome c and microscopic dielectric effects in proteins. (1986) (185)
- Coarse-grained (multiscale) simulations in studies of biophysical and chemical systems. (2011) (184)
- Langevin Dipoles Model for ab Initio Calculations of Chemical Processes in Solution: Parametrization and Application to Hydration Free Energies of Neutral and Ionic Solutes and Conformational Analysis in Aqueous Solution (1997) (184)
- Spectroscopic properties of photosynthetic reaction centers. 2. Application of the theory to Rhodopseudomonas viridis (1987) (183)
- Simulation of the dynamics of electron transfer reactions in polar solvents: Semiclassical trajectories and dispersed polaron approaches (1986) (182)
- Calculations of resonance Raman spectra of conjugated molecules (1977) (181)
- Extreme conformational flexibility of the furanose ring in DNA and RNA (1978) (181)
- Absolute binding free energy calculations: On the accuracy of computational scoring of protein–ligand interactions (2010) (180)
- The effect of protein relaxation on charge-charge interactions and dielectric constants of proteins. (1998) (179)
- On the mechanism of hydrolysis of phosphate monoesters dianions in solutions and proteins. (2006) (178)
- Examining methods for calculations of binding free energies: LRA, LIE, PDLD‐LRA, and PDLD/S‐LRA calculations of ligands binding to an HIV protease (2000) (177)
- Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions (2011) (176)
- Spectroscopic properties of photosynthetic reaction centers. 1. Theory (1987) (172)
- Dispersed polaron simulations of electron transfer in photosynthetic reaction centers. (1989) (170)
- Multiscale modeling of biological functions: from enzymes to molecular machines (Nobel Lecture). (2014) (168)
- Phosphate Ester Hydrolysis in Aqueous Solution: Associative versus Dissociative Mechanisms (1998) (165)
- Computer simulations of electron-transfer reactions in solution and in photosynthetic reaction centers. (1991) (162)
- The empirical valence bond model: theory and applications (2011) (159)
- Molecular dynamics simulations of biological reactions. (2002) (158)
- The Reorganization Energy of Cytochrome c Revisited (1997) (154)
- Calculation of vibronic structure of the π→π* transition of trans‐ and cis‐stilbene (1975) (154)
- Dipoles localized at helix termini of proteins stabilize charges. (1991) (148)
- Perspective: Defining and quantifying the role of dynamics in enzyme catalysis. (2016) (147)
- Towards accurate ab initio QM/MM calculations of free-energy profiles of enzymatic reactions. (2006) (146)
- What really prevents proton transport through aquaporin? Charge self-energy versus proton wire proposals. (2003) (143)
- Evaluation of catalytic free energies in genetically modified proteins. (1988) (141)
- How Important Are Quantum Mechanical Nuclear Motions in Enzyme Catalysis (1996) (141)
- Simulating the dynamics of the primary charge separation process in bacterial photosynthesis (1988) (140)
- Energy storage and reaction pathways in the first step of the vision process (1982) (138)
- How important are entropic contributions to enzyme catalysis? (2000) (137)
- On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions. (2005) (136)
- How does GAP catalyze the GTPase reaction of Ras? A computer simulation study. (2000) (134)
- Microscopic Calculations of Solvent Effects on Absorption Spectra of Conjugated Molecules (1991) (134)
- Ab Initio Free Energy Perturbation Calculations of Solvation Free Energy Using the Frozen Density Functional Approach (1994) (133)
- Calculations of Activation Entropies of Chemical Reactions in Solution (2000) (131)
- Simulations of quantum mechanical corrections for rate constants of hydride-transfer reactions in enzymes and solutions (1991) (130)
- The low barrier hydrogen bond (LBHB) proposal revisited: The case of the Asp ··· His pair in serine proteases (2004) (130)
- Hybrid ab Initio Quantum Mechanics/Molecular Mechanics Calculations of Free Energy Surfaces for Enzymatic Reactions: The Nucleophilic Attack in Subtilisin (1998) (130)
- Free energy relationships in metalloenzyme-catalyzed reactions. Calculations of the effects of metal ion substitutions in staphylococcal nuclease (1990) (129)
- Consistent force field for calculation of vibrational spectra and conformations of some amides and lactam rings (1970) (129)
- Ab Initio Calculations of Free Energy Barriers for Chemical Reactions in Solution (1995) (128)
- Energy considerations show that low-barrier hydrogen bonds do not offer a catalytic advantage over ordinary hydrogen bonds. (1996) (125)
- Simulations of the large kinetic isotope effect and the temperature dependence of the hydrogen atom transfer in lipoxygenase. (2004) (125)
- Ab Initio QM/MM Simulation with Proper Sampling: “First Principle” Calculations of the Free Energy of the Autodissociation of Water in Aqueous Solution (2002) (124)
- Interpretation of resonance Raman spectra of biological molecules. (1977) (122)
- Thermodynamic Parameters for Stacking and Hydrogen Bonding of Nucleic Acid Bases in Aqueous Solution: Ab Initio/Langevin Dipoles Study (1999) (121)
- Structure/function correlations of proteins using MM, QM/MM, and related approaches: methods, concepts, pitfalls, and current progress. (2003) (121)
- Computer simulation of the chemical catalysis of DNA polymerases: discriminating between alternative nucleotide insertion mechanisms for T7 DNA polymerase. (2003) (120)
- The barrier for proton transport in aquaporins as a challenge for electrostatic models: The role of protein relaxation in mutational calculations (2006) (119)
- Dynamics of enzymatic reactions. (1984) (117)
- Theoretical correlation of structure and energetics in the catalytic reaction of trypsin (1986) (116)
- Nature of the Surface Crossing Process in Bacteriorhodopsin: Computer Simulations of the Quantum Dynamics of the Primary Photochemical Event (2001) (116)
- Energetics of ion permeation through membrane channels. Solvation of Na+ by gramicidin A. (1989) (115)
- On the mechanism of guanosine triphosphate hydrolysis in ras p21 proteins. (1992) (115)
- On the action of cytochrome c: correlating geometry changes upon oxidation with activation energies of electron transfer (1983) (114)
- Why have mutagenesis studies not located the general base in ras p21 (1994) (113)
- Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase (2010) (112)
- Apparent NAC effect in chorismate mutase reflects electrostatic transition state stabilization. (2003) (111)
- Protein control of iron-sulfur cluster redox potentials. (1992) (111)
- Mechanistic alternatives in phosphate monoester hydrolysis: what conclusions can be drawn from available experimental data? (1999) (109)
- Origin of the temperature dependence of isotope effects in enzymatic reactions: the case of dihydrofolate reductase. (2007) (105)
- Paradynamics: an effective and reliable model for ab initio QM/MM free-energy calculations and related tasks. (2011) (104)
- Electron-transfer pathways in the primary event of bacterial photosynthesis (1988) (104)
- Vibrational structure of electronic transitions in conjugated molecules (1972) (103)
- Calculation of pi-pi excited state conformations and vibronic structure of retinal and related molecules. (1974) (103)
- A Quantized Classical Path Approach for Calculations of Quantum Mechanical Rate Constants (1993) (103)
- What are the roles of substrate-assisted catalysis and proximity effects in peptide bond formation by the ribosome? (2005) (102)
- Incorporating electric polarizabilities in water-water interaction potentials (1990) (102)
- Structure-energy analysis of the role of metal ions in phosphodiester bond hydrolysis by DNA polymerase I (1995) (101)
- CONVERSION OF LIGHT ENERGY TO ELECTROSTATIC ENERGY IN THE PROTON PUMP OF HALOBACTERIUM HALOBIUM (1979) (101)
- Remarkable rate enhancement of orotidine 5'-monophosphate decarboxylase is due to transition-state stabilization rather than to ground-state destabilization. (2000) (97)
- The Physics and Physical Chemistry of Molecular Machines. (2016) (97)
- Calculations of Hydration Entropies of Hydrophobic, Polar, and Ionic Solutes in the Framework of the Langevin Dipoles Solvation Model (1999) (97)
- On the interpretation of the observed linear free energy relationship in phosphate hydrolysis: a thorough computational study of phosphate diester hydrolysis in solution. (2008) (95)
- Enzymes work by solvation substitution rather than by desolvation. (1989) (95)
- Charge stabilization mechanism in the visual and purple membrane pigments. (1978) (94)
- Calculations of Electrostatic Energies in Photosynthetic Reaction Centers (1995) (94)
- Role of arginine-38 in regulation of the cytochrome c oxidation-reduction equilibrium. (1989) (93)
- How much do enzymes really gain by restraining their reacting fragments? (2002) (92)
- Computer simulations of enzyme catalysis: finding out what has been optimized by evolution. (1998) (92)
- Using the constrained DFT approach in generating diabatic surfaces and off diagonal empirical valence bond terms for modeling reactions in condensed phases. (2006) (92)
- Modifying the beta,gamma leaving-group bridging oxygen alters nucleotide incorporation efficiency, fidelity, and the catalytic mechanism of DNA polymerase beta. (2007) (90)
- Quantum corrections for rate constants of diabatic and adiabatic reactions in solutions (1990) (90)
- Q-Chem 2.0: a high-performance ab initio electronic structure program package (2000) (89)
- Computer simulation of the initial proton transfer step in human carbonic anhydrase I. (1992) (89)
- Why does the Ras switch “break” by oncogenic mutations? (2004) (89)
- Simulations of ion current in realistic models of ion channels: The KcsA potassium channel (2002) (89)
- The catalytic effect of dihydrofolate reductase and its mutants is determined by reorganization energies. (2007) (88)
- Electrostatic origin of the mechanochemical rotary mechanism and the catalytic dwell of F1-ATPase (2011) (88)
- Semiquantitative calculations of catalytic free energies in genetically modified enzymes. (1987) (87)
- Role of solvent reorganization energies in the catalytic activity of enzymes (1991) (86)
- On the relationship between thermal stability and catalytic power of enzymes. (2007) (86)
- Origin of the catalytic power of acetylcholinesterase: Computer simulation studies (1998) (85)
- The EVB as a quantitative tool for formulating simulations and analyzing biological and chemical reactions. (2010) (85)
- Computer simulations of protein functions: searching for the molecular origin of the replication fidelity of DNA polymerases. (2005) (84)
- Ab-initio Frozen Density Functional Calculations of Proton Transfer Reactions in Solution (1996) (84)
- Exploring the Dependence of QM/MM Calculations of Enzyme Catalysis on the Size of the QM Region (2016) (83)
- Transition state theory can be used in studies of enzyme catalysis: lessons from simulations of tunnelling and dynamical effects in lipoxygenase and other systems (2006) (82)
- Exploring the origin of the ion selectivity of the KcsA potassium channel (2003) (82)
- A microscopic model for calculations of chemical processes in aqueous solutions (1978) (81)
- Electrostatic basis for the unidirectionality of the primary proton transfer in cytochrome c oxidase (2008) (79)
- Ketosteroid isomerase provides further support for the idea that enzymes work by electrostatic preorganization (2010) (79)
- Electrostatic contributions to protein–protein binding affinities: Application to Rap/Raf interaction (1998) (79)
- The dynamics of the primary event in rhodopsins revisited (1991) (78)
- Energy-structure correlation in metalloporphyrins and the control of oxygen binding by hemoglobin. (1977) (78)
- Polarization constraints in molecular dynamics simulation of aqueous solutions: The surface constraint all atom solvent (SCAAS) model (1985) (78)
- Magnesium-cationic dummy atom molecules enhance representation of DNA polymerase beta in molecular dynamics simulations: improved accuracy in studies of structural features and mutational effects. (2007) (78)
- On the relationship between folding and chemical landscapes in enzyme catalysis (2008) (78)
- Semiclassical trajectory approach to photoisomerization (1975) (77)
- Associative versus dissociative mechanisms of phosphate monoester hydrolysis: on the interpretation of activation entropies. (2008) (76)
- Examining the case for the effect of barrier compression on tunneling, vibrationally enhanced catalysis, catalytic entropy and related issues (2010) (76)
- Mechanistic analysis of the observed linear free energy relationships in p21ras and related systems. (1996) (76)
- What about protein polarity? (1987) (76)
- Monte Carlo simulations of proton pumps: on the working principles of the biological valve that controls proton pumping in cytochrome c oxidase. (2006) (76)
- Studies of proton translocations in biological systems: simulating proton transport in carbonic anhydrase by EVB-based models. (2004) (75)
- DNA polymerase beta fidelity: halomethylene-modified leaving groups in pre-steady-state kinetic analysis reveal differences at the chemical transition state. (2008) (75)
- A new paradigm for electrostatic catalysis of radical reactions in vitamin B12 enzymes (2007) (75)
- Why ion pair reversal by protein engineering is unlikely to succeed (1988) (73)
- Ab Initio Evaluation of the Potential Surface for General Base- Catalyzed Methanolysis of Formamide: A Reference Solution Reaction for Studies of Serine Proteases (2000) (72)
- Calculations of free energy profiles for the staphylococcal nuclease catalyzed reaction. (1989) (71)
- Calculation of the redox potentials of iron-sulfur proteins: the 2-/3-couple of [Fe4S*4Cys4] clusters in Peptococcus aerogenes ferredoxin, Azotobacter vinelandii ferredoxin I, and Chromatium vinosum high-potential iron protein. (1994) (71)
- Intermolecular Potentials for N2 Molecules and the Lattice Vibrations of Solid α‐N2 (1970) (71)
- Simulating proton translocations in proteins: Probing proton transfer pathways in the Rhodobacter sphaeroides reaction center (1999) (70)
- Computer aided enzyme design and catalytic concepts. (2014) (70)
- Calculations of ground- and excited-state potential surfaces for conjugated heteroatomic molecules (1981) (69)
- A fast estimate of electrostatic group contributions to the free energy of protein-inhibitor binding. (1997) (69)
- Quantitative exploration of the molecular origin of the activation of GTPase (2013) (68)
- Reorganization energy of the initial electron-transfer step in photosynthetic bacterial reaction centers. (1998) (68)
- Linear free energy relationships in the intrinsic and GTPase activating protein-stimulated guanosine 5'-triphosphate hydrolysis of p21ras. (1996) (68)
- Converting structural information into an allosteric-energy-based picture for elongation factor Tu activation by the ribosome (2011) (68)
- Challenges and advances in validating enzyme design proposals: the case of kemp eliminase catalysis. (2011) (67)
- Converting conformational changes to electrostatic energy in molecular motors: The energetics of ATP synthase (2003) (66)
- Role of the chlorophyll dimer in bacterial photosynthesis. (1980) (66)
- 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 (1993) (66)
- Microscopic and semimacroscopic redox calculations: what can and cannot be learned from continuum models (1997) (65)
- On the origin of the electrostatic barrier for proton transport in aquaporin (2004) (65)
- Theoretical evaluation of potential surfaces, equilibrium geometries and vibronic transition intensities of excimers: the pyrene crystal excimer (1974) (65)
- Solute solvent dynamics and energetics in enzyme catalysis: the S(N)2 reaction of dehalogenase as a general benchmark. (2004) (65)
- A new view of the dynamics of singlet cis-trans photoisomerization (1979) (64)
- Theoretical studies of the visual chromophore (1975) (64)
- Orientation of the OH Dipole of Tyrosine (M)210 and Its Effect on Electrostatic Energies in Photosynthetic Bacterial Reaction Centers (1996) (64)
- Are mixed explicit/implicit solvation models reliable for studying phosphate hydrolysis? A comparative study of continuum, explicit and mixed solvation models. (2009) (64)
- A Fundamental Assumption about OH- Attack in Phosphate Ester Hydrolysis Is Not Fully Justified (1997) (63)
- Folding and stability of helical proteins: carp myogen. (1976) (62)
- Multiscale simulations of protein landscapes: Using coarse‐grained models as reference potentials to full explicit models (2010) (59)
- Protein Control of Redox Potentials of Iron‐Sulfur Proteins (1997) (58)
- 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. (2007) (58)
- 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. (2006) (58)
- A density-matrix model of photosynthetic electron transfer with microscopically estimated vibrational relaxation times (2004) (56)
- Exploring, refining, and validating the paradynamics QM/MM sampling. (2012) (56)
- Quantum-mechanical calculations of solvation free energies. A combined ab initio pseudopotential free-energy perturbation approach (1992) (56)
- Monte Carlo Calculations (2002) (56)
- Computational Approaches to Biochemical Reactivity (2002) (55)
- Theoretical Investigation of the Binding Free Energies and Key Substrate-Recognition Components of the Replication Fidelity of Human DNA Polymerase β (2002) (55)
- Addressing open questions about phosphate hydrolysis pathways by careful free energy mapping. (2013) (55)
- CALCULATION OF PI,PI(*) EXCITED STATE CONFORMATIONS AND VIBRONIC STRUCTURE OF RETINAL AND RELATED MOLECULES (1974) (54)
- Using a charging coordinate in studies of ionization induced partial unfolding. (2006) (54)
- Realistic simulations of proton transport along the gramicidin channel: demonstrating the importance of solvation effects. (2005) (53)
- Multiscale modeling of biological functions. (2011) (53)
- Simulating redox coupled proton transfer in cytochrome c oxidase: Looking for the proton bottleneck (2005) (53)
- Effect of the Asn52----Ile mutation on the redox potential of yeast cytochrome c. Theory and experiment. (1992) (53)
- Effective approach for calculations of absolute stability of proteins using focused dielectric constants (2009) (52)
- Methyltransferases do not work by compression, cratic, or desolvation effects, but by electrostatic preorganization (2015) (52)
- Computer simulations of enzymatic reactions: examination of linear free-energy relationships and quantum-mechanical corrections in the initial proton-transfer step of carbonic anhydrase. (1992) (52)
- Realistic simulations of the coupling between the protomotive force and the mechanical rotation of the F0-ATPase (2012) (52)
- A comprehensive examination of the contributions to the binding entropy of protein–ligand complexes (2010) (50)
- Ab Initio Evaluation of the Free Energy Surfaces for the General Base/Acid Catalyzed Thiolysis of Formamide and the Hydrolysis of Methyl Thiolformate: A Reference Solution Reaction for Studies of Cysteine Proteases (2001) (50)
- Dependence of Photosynthetic Electron-Transfer Kinetics on Temperature and Energy in a Density-Matrix Model† (2004) (49)
- Computer Simulation Studies of the Catalytic Mechanism of Human Aldose Reductase (2000) (49)
- Electrostatic contributions to protein stability and folding energy (2007) (49)
- Toward computer-aided site-directed mutagenesis of enzymes. (1986) (48)
- Toward accurate screening in computer-aided enzyme design. (2009) (48)
- Using simplified protein representation as a reference potential for all-atom calculations of folding free energy (1999) (48)
- Conformational Flexibility of Phosphate, Phosphonate, and Phosphorothioate Methyl Esters in Aqueous Solution (1998) (47)
- The origin of the red shift of the absorption spectra of aggregated chlorophylls (1979) (47)
- On the Reactivity of Phosphate Monoester Dianions in Aqueous Solution: Brønsted Linear Free-Energy Relationships Do Not Have an Unique Mechanistic Interpretation (1998) (47)
- Simulating electrostatic energies in proteins: Perspectives and some recent studies of pKas, redox, and other crucial functional properties (2011) (46)
- Accelerating QM/MM free energy calculations: representing the surroundings by an updated mean charge distribution. (2008) (46)
- The surface constraint all atom model provides size independent results in calculations of hydration free energies (1998) (46)
- Quantifying the mechanism of phosphate monoester hydrolysis in aqueous solution by evaluating the relevant ab initio QM/MM free-energy surfaces. (2013) (45)
- Free-Energy Perturbation Calculations of DNA Destabilization by Base Substitutions: The Effect of Neutral Guanine·Thymine, Adenine·Cytosine and Adenine·Difluorotoluene Mismatches (2000) (45)
- Exploration of the cytochrome c oxidase pathway puzzle and examination of the origin of elusive mutational effects. (2011) (45)
- KINETIC AND SPECTROSCOPIC EFFECTS OF PROTEIN‐CHROMOPHORE ELECTROSTATIC INTERACTIONS IN BACTERIORHODOPSIN (1979) (44)
- Dineopentyl phosphate hydrolysis: evidence for stepwise water attack. (2008) (44)
- Dissecting the role of the γ-subunit in the rotary–chemical coupling and torque generation of F1-ATPase (2015) (44)
- On the energetics of translocon-assisted insertion of charged transmembrane helices into membranes (2010) (43)
- Energetics of heme-protein interactions in hemoglobin (1981) (43)
- Effects of solute–solvent coupling and solvent saturation on solvation dynamics of charge transfer reactions (1988) (43)
- Exploring pathways and barriers for coupled ET/PT in cytochrome c oxidase: a general framework for examining energetics and mechanistic alternatives. (2007) (43)
- Electrostatic control of GTP and GDP binding in the oncoprotein p21ras. (1996) (42)
- Towards Quantitative Computer‐Aided Studies of Enzymatic Enantioselectivity: The Case of Candida antarctica Lipase A (2012) (42)
- Quantifying free energy profiles of proton transfer reactions in solution and proteins by using a diabatic FDFT mapping. (2008) (42)
- Mechanism of Charge Separation in Purple Bacterial Reaction Centers (2009) (42)
- Electrostatic control of the efficiency of light-induced electron transfer across membranes. (1981) (41)
- 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. (2010) (40)
- Analyzing Free Energy Relationships for Proton Translocations in Enzymes: Carbonic Anhydrase Revisited (2004) (40)
- CONTINUUM AND DIPOLE-LATTICE MODELS OF SOLVATION (1997) (39)
- The extended Ewald method: A general treatment of long‐range electrostatic interactions in microscopic simulations (1988) (39)
- Capturing the energetics of water insertion in biological systems: The water flooding approach (2013) (39)
- An effective Coarse‐grained model for biological simulations: Recent refinements and validations (2014) (38)
- The energetics of the primary proton transfer in bacteriorhodopsin revisited: it is a sequential light-induced charge separation after all. (2008) (37)
- Predicting drug-resistant mutations of HIV protease. (2008) (37)
- Exploring the role of large conformational changes in the fidelity of DNA polymerase β (2007) (36)
- Proton-transport mechanisms in cytochrome c oxidase revealed by studies of kinetic isotope effects. (2011) (36)
- Pair-states in α-perylene crystal. A theoretical study (1978) (35)
- Energetics of Cation Radical Formation at the Proximal Active Site Tryptophan of Cytochrome c Peroxidase and Ascorbate Peroxidase (1998) (35)
- Prechemistry versus preorganization in DNA replication fidelity (2011) (35)
- An Analysis of All the Relevant Facts and Arguments Indicates that Enzyme Catalysis Does Not Involve Large Contributions from Nuclear Tunneling. (2010) (35)
- Critical Differences between the Binding Features of the Spike Proteins of SARS-CoV-2 and SARS-CoV (2020) (35)
- Exploring the Mechanism of Covalent Inhibition: Simulating the Binding Free Energy of α-Ketoamide Inhibitors of the Main Protease of SARS-CoV-2 (2020) (34)
- Refining the treatment of membrane proteins by coarse‐grained models (2016) (34)
- Simulation of tunneling in enzyme catalysis by combining a biased propagation approach and the quantum classical path method: application to lipoxygenase. (2008) (34)
- On the energetics of the primary electron-transfer process in bacterial reaction centers (1994) (34)
- Energetics of the Catalytic Reaction of Ribonuclease A: A Computational Study of Alternative Mechanisms (1998) (33)
- Computer simulation studies of the fidelity of DNA polymerases (2003) (33)
- Constraining the electron densities in DFT method as an effective way for ab initio studies of metal‐catalyzed reactions (2000) (33)
- Exploring the free-energy landscape of GPCR activation (2018) (32)
- 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. (2005) (32)
- On the energetics of ATP hydrolysis in solution. (2009) (32)
- Realistic simulation of the activation of voltage-gated ion channels (2012) (31)
- LINEAR FREE ENERGY RELATIONSHIPS WITH QUANTUM MECHANICAL CORRECTIONS : CLASSICAL AND QUANTUM MECHANICAL RATE CONSTANTS FOR HYDRIDE TRANSFER BETWEEN NA D+ ANALOGUES IN SOLUTIONS (1995) (31)
- Revisiting the protomotive vectorial motion of F0-ATPase (2019) (30)
- Computer simulations of enzymatic reactionsCurrent Opinion in Structural Biology 1992, 2:230236 (1992) (30)
- Prechemistry barriers and checkpoints do not contribute to fidelity and catalysis as long as they are not rate limiting (2012) (29)
- Coarse grained model for exploring voltage dependent ion channels. (2012) (29)
- EMPIRICAL VALENCE BOND CALCULATIONS OF ENZYME CATALYSIS * (1981) (29)
- the Carbonium Ion in the (1976) (29)
- Simulating the electrostatic guidance of the vectorial translocations in hexameric helicases and translocases (2009) (29)
- A STRINGENT TEST OF THE CAVITY CONCEPT IN CONTINUUM DIELECTRICS (1997) (28)
- Coarse-grained simulations of the gating current in the voltage-activated Kv1.2 channel (2014) (28)
- Circe Effect versus Enzyme Preorganization: What Can Be Learned from the Structure of the Most Proficient Enzyme? (2001) (28)
- Toward accurate microscopic calculation of solvation entropies: extending the restraint release approach to studies of solvation effects. (2009) (27)
- On unjustifiably misrepresenting the EVB approach while simultaneously adopting it. (2009) (26)
- LINEAR FREE ENERGY RELATIONSHIPS IN ENZYMES. THEORETICAL ANALYSIS OF THE REACTION OF TYROSYL-TRNA SYNTHETASE (1994) (26)
- Simulating the dynamics of the mechanochemical cycle of myosin-V (2017) (26)
- Oxidation of 4a,4b‐Dihydrophenanthrenes. III. A Theoretical Study of the Large Kinetic Isotope Effect of Deuterium in the Initiation Step of the Thermal Reaction with Oxygen (1970) (26)
- Exploring the Development of Ground-State Destabilization and Transition-State Stabilization in Two Directed Evolution Paths of Kemp Eliminases. (2017) (26)
- On the Generation of Catalytic Antibodies by Transition State Analogues (2003) (26)
- Dynamical Contributions to Enzyme Catalysis: Critical Tests of a Popular Hypothesis (2006) (26)
- Exploring the nature of the translocon-assisted protein insertion (2012) (26)
- Molecular Dynamics Free-Energy Simulations of the Binding Contribution to the Fidelity of T7 DNA Polymerase (2002) (26)
- Molecular inelastic neutron scattering: Computational methods using consistent force fields (1974) (25)
- The entropic contributions in vitamin B12 enzymes still reflect the electrostatic paradigm (2015) (25)
- Reply to Karplus: Conformational dynamics have no role in the chemical step (2010) (25)
- Multiscale Modeling of Biological Functions: From Enzymes to Molecular Machines (Nobel Lecture) (2014) (25)
- [42] Correlation between the structure and efficiency of light-induced proton pumps (1986) (24)
- Coupling of charge stabilization, torsion and bond alternation in light-induced reactions of visual pigments (1978) (24)
- Quantum Mechanical Consistent Force Field (QCFF/PI) Method: Calculations of Energies, Conformations and Vibronic Interactions of Ground and Excited States of Conjugated Molecules (1973) (24)
- Calculations of Spectroscopic Properties of Bacterial Reaction Centers (1985) (24)
- The FOF1 ATP synthase: from atomistic three-dimensional structure to the rotary-chemical function (2017) (24)
- Enhancing Paradynamics for QM/MM Sampling of Enzymatic Reactions. (2016) (24)
- Neural Networks and Genetic Algorithms (2002) (24)
- Renormalizing SMD: the renormalization approach and its use in long time simulations and accelerated PMF calculations of macromolecules. (2010) (23)
- Misunderstanding the preorganization concept can lead to confusions about the origin of enzyme catalysis (2017) (23)
- Simulating the fidelity and the three Mg mechanism of pol η and clarifying the validity of transition state theory in enzyme catalysis (2017) (23)
- Origin of Linear Free Energy Relationships: Exploring the Nature of the Off-Diagonal Coupling Elements in SN2 Reactions (2012) (23)
- Exploring the challenges of computational enzyme design by rebuilding the active site of a dehalogenase (2018) (23)
- Electrostatic origin of the catalytic effect of a supramolecular host catalyst. (2012) (22)
- ZnT2 is an electroneutral proton-coupled vesicular antiporter displaying an apparent stoichiometry of two protons per zinc ion (2019) (22)
- Electrostatic origin of the unidirectionality of walking myosin V motors (2013) (22)
- Predicting Mutational Effects on Receptor Binding of the Spike Protein of SARS-CoV-2 Variants (2021) (21)
- Effective Methods for Estimation of Binding Energies in Computer‐Aided Drug Design (1994) (21)
- Computer Simulation of Enzymatic Reactions (1986) (21)
- The ClCFF/PI+ MGA program package efficiency and versatility in molecular mechanics (1977) (21)
- Simulating the pulling of stalled elongated peptide from the ribosome by the translocon (2013) (21)
- Simulating the function of sodium/proton antiporters (2015) (21)
- On the control of the proton current in the voltage-gated proton channel Hv1 (2018) (21)
- Simulating large nuclear quantum mechanical corrections in hydrogen atom transfer reactions in metalloenzymes (2004) (20)
- Exploring the Catalytic Mechanism of Cas9 Using Information Inferred from Endonuclease VII. (2018) (20)
- A computational study of the hydrolysis of dGTP analogues with halomethylene-modified leaving groups in solution: implications for the mechanism of DNA polymerases. (2009) (20)
- On the molecular origin of the anomalous polarization in the resonance raman of metalloporphyrins (1976) (20)
- DNA polymerase β catalytic efficiency mirrors the Asn279–dCTP H‐bonding strength (2007) (20)
- Simulating the Energetics and Dynamics of Enzymatic Reactions (1984) (20)
- Torque, chemistry and efficiency in molecular motors: a study of the rotary–chemical coupling in F1-ATPase (2015) (20)
- A binding free energy decomposition approach for accurate calculations of the fidelity of DNA polymerases (2009) (19)
- Theoretical study of excimers in crystals of flexible conjugated molecules. Excimer formation and photodimerization in crystalline 1,4-diphenylbutadiene (1975) (18)
- EFFECT OF SOLVENT DISCRETENESS ON SOLVATION (1998) (18)
- Semiclassical calculation of electronic spectra of supercooled anharmonic molecules (1983) (18)
- Phosphate ester analogues as probes for understanding enzyme catalysed phosphoryl transfer (2010) (18)
- Exploring the mechanism of DNA polymerases by analyzing the effect of mutations of active site acidic groups in Polymerase β (2016) (17)
- Calculations of the electrostatic free energy contributions to the binding free energy of sulfonamides to carbonic anhydrase (1996) (16)
- Role of active site residues in the glycosylase step of T4 endonuclease V. Computer simulation studies on ionization states. (1999) (16)
- Computer modeling of enzyme catalysis and its relationship to concepts in physical organic chemistry (2005) (16)
- Effective way of modeling chemical catalysis: Empirical valence bond picture of role of solvent and catalyst in alkylation reactions (2000) (16)
- EF-Tu and EF-G are activated by allosteric effects (2018) (16)
- Calculation of the Anharmonicity in the Vibrational Frequencies of Alkane Molecules by the CFF Functions (1971) (16)
- An empirical function for second neighbor interactions and its effect on vibrational modes and other properties of cyclo- and n-Alkanes (1969) (16)
- On the origin of the catalytic power of carboxypeptidase A and other metalloenzymes (2009) (16)
- Catalytic Hydrolysis of Adenosine 2‘,3‘-Cyclic Monophosphate by CuII Terpyridine (1999) (16)
- On the challenge of exploring the evolutionary trajectory from phosphotriesterase to arylesterase using computer simulations. (2015) (16)
- Quantized semiclassical trajectory approach for evaluation of vibronic transitions in anharmonic molecules (1985) (15)
- Electrostatic basis for bioenergetics. (2004) (15)
- The Empirical Valence Bond (EVB) Method (2004) (15)
- Energetics of Light-Induced Charge Separation Across Membranes (1981) (15)
- Reexamining the origin of the directionality of myosin V (2017) (15)
- The resonance Raman spectrum of azulene (1976) (15)
- Validating computer simulations of enantioselective catalysis; reproducing the large steric and entropic contributions in Candida Antarctica lipase B (2014) (15)
- Calculations of Electrostatic Energies in Proteins Using Microscopic, Semimicroscopic and Macroscopic Models and Free-Energy Perturbation Approaches (2008) (14)
- Quantum Mechanical-Molecular Mechanical Approaches for Studying Chemical Reactions in Proteins and Solution (1998) (14)
- The Consistent Force Field and Its Quantum Mechanical Extension (1977) (14)
- Theory and applications of the empirical valence bond approach : from physical chemistry to chemical biology (2017) (14)
- Incorporation of inter- and intramolecular forces in the calculation of crystal packing and lattice vibrations (1974) (14)
- Calculations of charge-transfer transition energies and spectroscopic properties of a molecular crystal: methylbacteriopheophorbide a (1989) (13)
- Origin of the Non-Arrhenius Behavior of the Rates of Enzymatic Reactions. (2017) (13)
- Examination of intramolecular potential surfaces of flexible conjugated molecules by calculation of crystal structures. equilibrium geometries of chalc (1974) (13)
- Catalytic effects of mutations of distant protein residues in human DNA polymerase β: theory and experiment. (2012) (13)
- Exploring the Catalytic Reaction of Cysteine Proteases. (2020) (12)
- Simulations of Electron Transfer in Bacterial Reaction Centers (1993) (12)
- Constraining the electron densities in DFT method as an effective way for ab initio studies of metal-catalyzed reactions (2000) (12)
- Modeling gating charge and voltage changes in response to charge separation in membrane proteins (2014) (12)
- Resonance raman spectrum of azulene (1978) (12)
- Validating the vitality strategy for fighting drug resistance (2012) (12)
- Exploring alternative catalytic mechanisms of the Cas9 HNH domain (2020) (12)
- Validating the Water Flooding Approach by Comparing It to Grand Canonical Monte Carlo Simulations. (2017) (11)
- Calculations of Solvation Free Energies in Chemistry and Biology. (1995) (11)
- Computer Simulations of Electron-Transfer Reactions in Solution and in Photosynthetic Reaction Centers (1992) (11)
- Solvation free energies of molecules. The most stable anionic tautomers of uracil. (2008) (11)
- On the relationship between the dispersed polaron and spin-boson models (1997) (11)
- Demonstrating aspects of multiscale modeling by studying the permeation pathway of the human ZnT2 zinc transporter (2018) (10)
- Comment on “a fast and simple method to calculate protonation states in proteins” (2000) (10)
- Anharmonicity in Crystal Vibrations (1971) (10)
- The empirical valence bond as an effective strategy for computer-aided enzyme design. (2009) (10)
- Oscillations of the energy gap for the initial electron-transfer step in bacterial reaction centers (1998) (10)
- Calculations of CD and CPL spectra as a tool for evaluation of the conformational differences between ground and excited states of chiral molecules (1974) (10)
- Electrostatic Effects on the Speed and Directionality of Electron Transfer in Bacterial Reaction Centers: The Special Role of Tyrosine M-208 (1990) (10)
- Macroscopic and Microscopic Estimates of the Energetics of Charge Separation in Bacterial Reaction Centers (1996) (9)
- Combinatorial Approach for Exploring Conformational Space and Activation Barriers in Computer-Aided Enzyme Design. (2020) (9)
- Exploring the Proteolysis Mechanism of the Proteasomes. (2020) (9)
- Electrostatics of Proteins: Principles, Models and Applications (2008) (9)
- Electrostatic influence on IL-1 transport through the GSDMD pore (2022) (9)
- Chapter 15:Challenges and Progresses in Calculations of Binding Free Energies – What Does it Take to Quantify Electrostatic Contributions to Protein–Ligand Interactions? (2007) (9)
- Exploring the activation pathway and Gi-coupling specificity of the μ-opioid receptor (2020) (9)
- Oxidation of 4a,4b‐Dihydrophenanthrene. IV. Kinetic Isotope Effect of Deuterium in the Propagation and the Initiation Steps (1970) (8)
- Converting structural changes upon oxidation of cytochrome c to electrostatic reorganization energy. (1983) (8)
- A free‐energy landscape for the glucagon‐like peptide 1 receptor GLP1R (2020) (8)
- Validating a Coarse-Grained Voltage Activation Model by Comparing Its Performance to the Results of Monte Carlo Simulations. (2017) (8)
- DNA polymerase beta catalytic efficiency mirrors the Asn279-dCTP H-bonding strength. (2007) (8)
- Computer Simulations of Isotope Effects in Enzyme Catalysis (2005) (8)
- Exploring the Effectiveness of Binding Free Energy Calculations. (2019) (8)
- Inverting the selectivity of aquaporin 6: gating versus direct electrostatic interaction. (2005) (8)
- Exploring the Drug Resistance of HCV Protease. (2017) (8)
- Exploring the Activation Process of the β2AR-Gs Complex. (2021) (8)
- Membranes Assembled from Narrow Carbon Nanotubes Block Proton Transport and Can Form Effective Nano-Filtration Devices (2006) (7)
- The control of the discrimination between dNTP and rNTP in DNA and RNA polymerase (2016) (7)
- The catalytic dwell in ATPases is not crucial for movement against applied torque (2020) (7)
- Brønsted slopes based on single-molecule imaging data help to unveil the chemically coupled rotation in F1-ATPase (2015) (7)
- A Microscopic Capacitor Model of Voltage Coupling in Membrane Proteins: Gating Charge Fluctuations in Ci-VSD. (2016) (6)
- Enhancing computational enzyme design by a maximum entropy strategy (2022) (6)
- Simulating the Catalytic Effect of a Designed Mononuclear Zinc Metalloenzyme that Catalyzes the Hydrolysis of Phosphate Triesters (2014) (6)
- Theoretical Analyses of Electron-Transfer Reactions (1995) (6)
- Ab initio/LD studies of chemical reactions in solution: Reference free‐energy surfaces for acylation reactions occurring in serine and cysteine proteases (2000) (6)
- Energetics and Dynamics of Transition States of Reactions in Enzymes and Solutions (1999) (6)
- Semiclassical simulations of the spectra of anharmonic molecules; problems and alternatives (1985) (6)
- Microscopic Based Density Matrix Treatments of Electron-Transfer Reactions in Condensed Phases (1999) (6)
- Progresses in Ab Initio QM/MM Free Energy Simulations of Electrostatic Energies in Proteins: Accelerated QM/MM Studies of pK (2009) (5)
- Simulating the Function of the MjNhaP1 Transporter. (2016) (5)
- Calculations of Spectroscopic Properties and Electron Transfer Kinetics of Photosynthetic Bacterial Reaction Centers (1987) (5)
- A new class of α-ketoamide derivatives with potent anticancer and anti-SARS-CoV-2 activities (2021) (5)
- Analyzing the electrogenicity of cytochrome c oxidase (2016) (5)
- Computer simulations of enzymatic reactions (1992) (5)
- Energetics of ion permeation through membrane channels (2005) (4)
- 1 THE CATALYTIC POWER OF DIHYDROFOLATE REDUCTASE AND OTHER ENZYMES ARISES FROM ELECTROSTATIC PREORGANIZATION , NOT CONFORMATIONAL MOTIONS (2013) (4)
- On the consistent calculation of lattice dynamics using semiempirical potential functions (1975) (4)
- Spectroscopic Properties and Electron Transfer Dynamics of Reaction Centers (1988) (4)
- Computer Simulations of Proton Transfer in Proteins and Solutions (2007) (4)
- Equilibrium fluctuation relations for voltage coupling in membrane proteins. (2015) (4)
- Consistent calculations of pK a 's of ionizable residues in proteins (1997) (4)
- Quantum catalysis: The modeling of catalytic transition states (1999) (3)
- On Possible Pitfalls in ab initio QM/MM Minimization Approaches For Studies of Enzymatic Reactions (2007) (3)
- Simulating the directional translocation of a substrate by the AAA+ motor in the 26S proteasome (2021) (3)
- Fast and Effective Prediction of the Absolute Binding Free Energies of Covalent Inhibitors of SARS-CoV-2 Main Protease and 20S Proteasome. (2022) (3)
- Protein Control of Redox Potentials of Ironminus signSulfur Proteins. (1996) (3)
- On the nature of the apparent free energy of inserting amino acids into membrane through the translocon. (2013) (3)
- Computer Simulations of the Action of Metalloenzymes (1997) (3)
- ON THE EFFICIENCY OF ELECTRON TRANSFER REACTIONS IN PROTEINS (1978) (3)
- A shortcut for multidimensional quantization. The average partial actions method (1985) (3)
- Two-dimensional free energy surfaces for primary electron transfer in a photosynthetic reaction center (1997) (2)
- Theoretical Correlation of Structure and Energetics in the Catalytic Reaction of Trypsin. (1987) (2)
- Chapter 1:Perspective on Computer Modelling of Enzymatic Reactions (2016) (2)
- Consistent calculations of electrostatic free energies in membrane channels. The solvation of Na+ by the gramicidin channel (1989) (2)
- Strain and Electrostatic Contributions to Cooperativity in Hemoglobin (1982) (2)
- Ab initio calculations of free energy barriers for chemical reactions in solution: proton transfer in [FHF]-. (1996) (2)
- Computer Simulation of Chemical Reactions in Synthetic Model Compounds and Genetically Engineered Active Sites (1988) (2)
- On the Origins of the Linear Free Energy Relationships: Exploring the Nature of the Off-Diagonal Coupling Elements in S(N)2 Reactions. (2012) (2)
- Calculations of chemical processes in solution by density-functional and other quantum-mechanical techniques (1997) (2)
- Analyzing the Reaction of Orotidine 5'-Phosphate Decarboxylase as a Way to Examine Some Key Catalytic Proposals. (2022) (2)
- QUANTUM-CHEMICAL INSIGHTS INTO MECHANISMS OF THE NONENZYMATIC HYDROLYSIS OF PHOSPHATE MONOESTERS (1999) (2)
- Additions and Corrections - Extreme Conformational Flexibility of the Furanose 2607 in DNA and RNA (1981) (1)
- Faculty Opinions recommendation of Anionic charge is prioritized over geometry in aluminum and magnesium fluoride transition state analogs of phosphoryl transfer enzymes. (2008) (1)
- Faculty Opinions recommendation of Substrate-assisted catalysis of peptide bond formation by the ribosome. (2004) (1)
- (lysozyme/enzyme mechanism/dielectric effects in enzymes and in solutions/relationship between protein folding and catalysis) (2004) (1)
- Microscopic Simulations of Chemical Reactions in Solutions and Protein Active Sites; Principles and Examples (1989) (1)
- Chapter 11:Tunnelling does not Contribute Significantly to Enzyme Catalysis, but Studying Temperature Dependence of Isotope Effects is Useful (2009) (1)
- Simulations of Proton Transfer and Hydride Transfer Reactions in Proteins (1992) (1)
- Primary Electron Transfer Mechanisms in Bacterial Reaction Centers (1990) (1)
- Spectroscopic Properties of Photosynthetic Reaction Centers. Part 1. Theory. (1988) (1)
- Optimal Protein Relaxation for Electron Transfer in Bacterial Photosynthesis (1982) (1)
- Response to Vilfan: Constructing structure-based free energy surfaces is the key to understand myosin V unidirectionality (2014) (1)
- Folding proteins along the dotted lines (reply) (1975) (1)
- THEORETICAL STUDY OF EXCIMERS IN CRYSTALS OF FLEXIBLE CONJUGATED MOLECULES, EXCIMER FORMATION AND PHOTODIMERIZATION IN CRYSTALLINE 1,4-DIPHENYLBUTADIENE (1975) (1)
- Spectroscopic Properties of Photosynthetic Reaction Centers. Part 2. Application of the Theory to Rhodopseudomonas viridis. (1988) (1)
- Microscopic simulation of quantum dynamics and nuclear tunneling in bacterial reaction centers (2004) (1)
- The FOF1 ATP synthase: from atomistic three-dimensional structure to the rotary-chemical function (2017) (1)
- SEMICLASSICAL SIMULATION OF VIBRONIC PROCESSES (1983) (1)
- Computer simulations of proton transfer in cytochrome c oxidase and nitric oxide reductase (2010) (1)
- Free Energy Functions for Charge Separation in Wild-Type and Mutant Bacterial Reaction Centers (1998) (1)
- Correction: Demonstrating aspects of multiscale modeling by studying the permeation pathway of the human ZnT2 zinc transporter (2019) (0)
- Simulation of Tunneling in Enzyme Catalysis: Application to Lipoxygenase (2006) (0)
- A Comprehensive Examination of the Contributions to Binding and Activation Entropies (2011) (0)
- Faculty Opinions recommendation of The first experimental test of the hypothesis that enzymes have evolved to enhance hydrogen tunneling. (2003) (0)
- Role of the Central Stalk in the Rotary-Chemical Coupling and Torque Generation of F1-ATPase (2016) (0)
- Molecular Dynamics Simulations of Biological Reactions (2010) (0)
- CALCULATION OF THE VIBRATIONAL SPECTRA OF EXCITED ELECTRONIC STATES OF CONJUGATED MOLECULES; ACCURATE EVALUATION OF VIBRONIC TRANSITION INTENSITIES (1971) (0)
- Role of Electrostatics in the Mechanochemical Rotary Mechanism of F1-ATPase (2012) (0)
- Computational Studies of Translocon-Assisted Processes of Membrane Protein Insertion and Translocation (2011) (0)
- Faculty Opinions recommendation of Inhibition of protein tyrosine phosphatase 1B and alkaline phosphatase by bis(maltolato)oxovanadium (IV). (2009) (0)
- Reviews of "Binding Profile Assessment of N501Y: a More Infectious Mutation on the Receptor Binding Domain of SARS-CoV-2 Spike Protein" (2021) (0)
- PREFACE (1993) (0)
- Effect of Environmental Factors on the Catalytic Activity of Intramembrane Serine Protease. (2022) (0)
- Faculty Opinions recommendation of High-energy intermediate or stable transition state analogue: theoretical perspective of the active site and mechanism of beta-phosphoglucomutase. (2004) (0)
- Realistic Modeling of Biological Motors; Electrostatic Origin of the Mechnochemical Rotatory Mechanism and the Catalytic Dwell of F1-ATPase (2012) (0)
- Exploring the Role of Chemical Reactions in the Selectivity of Tyrosine Kinase Inhibitors. (2022) (0)
- Calculations of the redox potentials of iron-sulfur proteins. (1993) (0)
- Perspective on “The energetics of enzymatic reactions” (2000) (0)
- The Mechanical Insights into Proton/Electron Transfer in Cytochrome C Oxidase Revealed by Direct Modeling of Voltage Changes in Response to Charge Separation (2016) (0)
- Electrostatic Contribution to the Transition States Binding Free Energy Using Simplified Coarse Grained Model (2010) (0)
- Calculations of redox potentials for the cluster in site directed mutants of Azotobacter vinelandii ferredoxin I (1995) (0)
- Stochastic QM/MM Models for Proton Transport in Condensed Phase: An Empirical Valence Bond (EVB) Approach (2005) (0)
- Faculty Opinions recommendation of A theoretical DFT investigation of the lysozyme mechanism: computational evidence for a covalent intermediate pathway. (2005) (0)
- Computational Enzyme Design: Refining Artificial Enzymes and Exploring Paths of Directed Evolution (2011) (0)
- Computational Approach to Study Membrane Protein Topology (2012) (0)
- Faculty Opinions recommendation of RanGAP mediates GTP hydrolysis without an arginine finger. (2002) (0)
- Ab initio Free Energies of Enzymatic Reactions Using Model Potentials (2005) (0)
- Faculty Opinions recommendation of Selective stabilization of the chorismate mutase transition state by a positively charged hydrogen bond donor. (2003) (0)
- Studying catalysis by QM/MM approaches should not be a black box process (2012) (0)
- 188 Using CG modeling in exploring the role of dynamical effects in catalysis and in simulating biological molecular machines (2013) (0)
- Faculty Opinions recommendation of Activation of orotidine 5'-monophosphate decarboxylase by phosphite dianion: the whole substrate is the sum of two parts. (2006) (0)
- Perspective on Calculations of Binding Free Energies (2017) (0)
- Activation Free Energies of Enzymatic Reactions; Simulations and Experiments (1987) (0)
- ELEC:TRON- TRANSFER REA<=TIONS IN SOLUTION AND IN PHOTOSYNTHETIC REA<=TION CENTERS (1991) (0)
- Theoretical studies of drug receptor interaction (1976) (0)
- Equilibrium Fluctuation Relations for Gating Charge in Voltage Sensitive Membrane Proteins: A Microscopic Capacitor Model Approach (2016) (0)
- Natural Evolution Provides Strong Hints about Laboratory Evolution of Designer Enzymes (2022) (0)
- Potential Functions (Force Fields) (2002) (0)
- Computational Study on the Catalytic Effect of the Magnesium Ions in the Mechanism of DNA Polymerases (2016) (0)
- Free Energy Calculations (2002) (0)
- DIRECT CALCULATION OF THE RESONANCE RAMAN SPECTRUM OF METALLOPORPHYRINS AND REPRODUCTION OF THE ANOMALOUS POLARIZATION EFFECT (1976) (0)
- Catalyst Modeling – Biological (2002) (0)
- Simulating the Dynamics of Electron Transfer Reactions in Cytochrome c (1987) (0)
- Enzyme Redesign: From Metal-Dependent to Metal-Independent, a Symphony Orchestra without Concertmasters (2018) (0)
- Reprint of: Semiclassical trajectory approach to photoisomerization (2013) (0)
- Harnessing natural evolution and computation towards systems enzymology. (2023) (0)
- Electrostatic influence of IL-1 transport through the GSDMD pore (2022) (0)
- Electrostatic Basis for Enzyme Catalysis (2006) (0)
- Challenges and advances in QM/MM methods for studies of energetics and dynamics of biological systems (2007) (0)
- Electrostatic Basis for Vectorial Light-Induced Charge Separation in Photobiological systems (1987) (0)
- A Structure Based Course-Graining Physical Modeling of the Voltage Activated Kv1.2 Channel - Simulating and Analyzing the Fast Gating Current (2014) (0)
- Corrections - Simulating the Dynamics of the Primary Charge Separation Process in Bacterial Photosynthesis (1989) (0)
- Faculty Opinions recommendation of Barriers to Hydride Transfer in Wild Type and Mutant Dihydrofolate Reductase from E. coli. (2003) (0)
- Using brain vs. brute force in computational studies of biological systems (2018) (0)
- Faculty Opinions recommendation of Dynamics of an enzymatic substitution reaction in haloalkane dehalogenase. (2004) (0)
- Combined AB initio and electrostatic calculations of tryptophan-191 oxidation in compound ES of cytochrome-c-peroxidase (1995) (0)
- Faculty Opinions recommendation of Does water relay play an important role in phosphoryl transfer reactions? Insights from theoretical study of a model reaction in water and tert-butanol. (2009) (0)
- External Electric Field in the Atomistic Simulation of Membrane Systems (2011) (0)
- From Kibbutz Fishponds to The Nobel Prize - Taking Molecular Functions into Cyberspace (2022) (0)
- Semiempirical and Ab Initio Modeling of Chemical Processes (1997) (0)
- CALCULATION OF VIBRONIC STRUCTURE OF THE PI-PI(*) TRANSITION OF TRANS- AND CIS-STILBENE (1975) (0)
- Pol β catalytic efficiency mirrors the Asn279-dCTP H-bonding strength (2007) (0)
- Theoretical modeling of the control of reduction potential of heme in cytochrome c peroxidase (1993) (0)
- Review 1: "Binding Profile Assessment of N501Y: a More Infectious Mutation on the Receptor Binding Domain of SARS-CoV-2 Spike Protein" (2021) (0)
- Electrostatic Basis of the Unidirectional Walking Motion in Myosin Molecular Motors (2014) (0)
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