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List of works by Arieh Warshel

A Microscopic Capacitor Model of Voltage Coupling in Membrane Proteins: Gating Charge Fluctuations in Ci-VSD

scientific article published on 30 December 2015

A binding free energy decomposition approach for accurate calculations of the fidelity of DNA polymerases

scientific article published on February 2010

A comprehensive examination of the contributions to the binding entropy of protein-ligand complexes

scientific article

A computational study of the hydrolysis of dGTP analogues with halomethylene-modified leaving groups in solution: implications for the mechanism of DNA polymerases

scientific article published on June 2009

A fast estimate of electrostatic group contributions to the free energy of protein-inhibitor binding ⬇️

scientific article published on December 1, 1997

A free-energy landscape for the glucagon-like peptide 1 receptor GLP1R

scientific article published on 02 August 2019

A new paradigm for electrostatic catalysis of radical reactions in vitamin B12 enzymes

scholarly article

Ab initio calculations of free energy barriers for chemical reactions in solution: proton transfer in [FHF]- ⬇️

scientific article published on January 1, 1996

Absolute binding free energy calculations: on the accuracy of computational scoring of protein-ligand interactions

scientific article

Accelerating QM/MM free energy calculations: representing the surroundings by an updated mean charge distribution

scientific article published on 16 April 2008

Addressing Open Questions about Phosphate Hydrolysis Pathways by Careful Free Energy Mapping ⬇️

scientific article published on December 28, 2012

Advances in methods and algorithms in a modern quantum chemistry program package.

scientific article

Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

article

An Analysis of All the Relevant Facts and Arguments Indicates that Enzyme Catalysis Does Not Involve Large Contributions from Nuclear Tunneling

scientific article published on July 2010

An effective coarse-grained model for biological simulations: recent refinements and validations

scientific article

Analyzing the electrogenicity of cytochrome c oxidase

scientific article published on 28 June 2016

Apparent NAC effect in chorismate mutase reflects electrostatic transition state stabilization

scientific article

Are mixed explicit/implicit solvation models reliable for studying phosphate hydrolysis? A comparative study of continuum, explicit and mixed solvation models

scientific article published in May 2009

Associative versus dissociative mechanisms of phosphate monoester hydrolysis: on the interpretation of activation entropies

scientific article published in August 2008

At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?

scientific article

Bicycle-pedal model for the first step in the vision process ⬇️

scientific article (publication date: 22 April 1976)

Brønsted slopes based on single-molecule imaging data help to unveil the chemically coupled rotation in F1-ATPase

scientific article published on 30 October 2015

Calculation of pi-pi excited state conformations and vibronic structure of retinal and related molecules

scientific article

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.

scientific article

Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603

scientific article published on April 1, 1992

Calculations of electrostatic energies in proteins. The energetics of ionized groups in bovine pancreatic trypsin inhibitor

Calculations of electrostatic interactions in biological systems and in solutions ⬇️

scientific article (publication date: August 1984)

Calculations of enzymatic reactions: calculations of pKa, proton transfer reactions, and general acid catalysis reactions in enzymes

scientific article published in May 1981

Calculations of free energy profiles for the staphylococcal nuclease catalyzed reaction

scientific article published in May 1989

Capturing the energetics of water insertion in biological systems: The water flooding approach ⬇️

scientific article published on September 28, 2012

Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions

scientific article

Catalytic Effects of Mutations of Distant Protein Residues in Human DNA Polymerase β: Theory and Experiment ⬇️

scientific article published on October 29, 2012

Challenges and Advances in Validating Enzyme Design Proposals: The Case of Kemp Eliminase Catalysis ⬇️

scientific article published on April 15, 2011

Charge stabilization mechanism in the visual and purple membrane pigments ⬇️

scientific article published on June 1, 1978

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 app

scientific article published in 1993

Circe effect versus enzyme preorganization: what can be learned from the structure of the most proficient enzyme?

scientific article published in February 2001

Coarse grained model for exploring voltage dependent ion channels ⬇️

scientific article published on August 5, 2011

Coarse-grained (multiscale) simulations in studies of biophysical and chemical systems

scientific article published on January 2011

Coarse-grained simulations of the gating current in the voltage-activated Kv1.2 channel

scientific article published on 24 January 2014

Comment on "a fast and simple method to calculate protonation states in proteins"

scientific article published on 01 July 2000

Computer Simulations of Electron-Transfer Reactions in Solution and in Photosynthetic Reaction Centers ⬇️

scientific article published on January 1, 1991

Computer aided enzyme design and catalytic concepts

scientific article

Computer simulation of protein folding

scientific article published on February 27, 1975

Computer simulation of the chemical catalysis of DNA polymerases: discriminating between alternative nucleotide insertion mechanisms for T7 DNA polymerase

scientific article published on July 2003

Computer simulation of the initial proton transfer step in human carbonic anhydrase I ⬇️

scientific article published on March 5, 1992

Computer simulation studies of the fidelity of DNA polymerases

scientific article published in March 2003

Computer simulations of enzymatic reactions: examination of linear free-energy relationships and quantum-mechanical corrections in the initial proton-transfer step of carbonic anhydrase

scientific article published on January 1, 1992

Computer simulations of enzyme catalysis: finding out what has been optimized by evolution.

scientific article

Computer simulations of enzyme catalysis: methods, progress, and insights

scientific article

Computer simulations of protein functions: searching for the molecular origin of the replication fidelity of DNA polymerases

scientific article

Conformation of retinal isomers

scientific article published in February 1974

Consistent Force Field Calculations. II. Crystal Structures, Sublimation Energies, Molecular and Lattice Vibrations, Molecular Conformations, and Enthalpies of Alkanes

scientific article (publication date: 15 July 1970)

Consistent Force Field for Calculations of Conformations, Vibrational Spectra, and Enthalpies of Cycloalkane and n‐Alkane Molecules

scientific article (publication date: December 1968)

Consistent force field for calculation of vibrational spectra and conformations of some amides and lactam rings

scientific article published in January 1970

Control of the redox potential of cytochrome c and microscopic dielectric effects in proteins

scientific article published in April 1986

Conversion of light energy to electrostatic energy in the proton pump of Halobacterium halobium

scientific article published on August 1, 1979

Converting conformational changes to electrostatic energy in molecular motors: The energetics of ATP synthase

scientific article

Converting structural changes upon oxidation of cytochrome c to electrostatic reorganization energy ⬇️

scientific article published on August 15, 1983

Converting structural information into an allosteric-energy-based picture for elongation factor Tu activation by the ribosome ⬇️

scientific article published on May 26, 2011

Correction to A Computational Study of the Hydrolysis of dGTP Analogues with Halomethylene-Modified Leaving Groups in Solution: Implications for the Mechanism of DNA Polymerases

scholarly article published in Biochemistry

Correction: Demonstrating aspects of multiscale modeling by studying the permeation pathway of the human ZnT2 zinc transporter

Critical Differences Between the Binding Features of the Spike Proteins of SARS-CoV-2 and SARS-CoV

scientific article published on 17 June 2020

DNA polymerase beta catalytic efficiency mirrors the Asn279-dCTP H-bonding strength

scientific article published on 25 January 2007

DNA polymerase beta fidelity: halomethylene-modified leaving groups in pre-steady-state kinetic analysis reveal differences at the chemical transition state

scientific article published on 28 December 2007

Demonstrating aspects of multiscale modeling by studying the permeation pathway of the human ZnT2 zinc transporter

scientific article published on 2 November 2018

Dineopentyl phosphate hydrolysis: evidence for stepwise water attack

scientific article published on 27 August 2008

Dipoles localized at helix termini of proteins stabilize charges

scientific article published on March 1991

Dispersed polaron simulations of electron transfer in photosynthetic reaction centers

scientific article published on 01 October 1989

Dissecting the role of the γ-subunit in the rotary-chemical coupling and torque generation of F1-ATPase

scientific article

Dynamical contributions to enzyme catalysis: critical tests of a popular hypothesis

scientific article (publication date: May 2006)

Dynamics of biochemical and biophysical reactions: insight from computer simulations

scientific article

Dynamics of enzymatic reactions

scientific article

EF-Tu and EF-G are activated by allosteric effects

scientific article published on 12 March 2018

Effect of the Asn52----Ile mutation on the redox potential of yeast cytochrome c. Theory and experiment

scientific article published on April 5, 1992

Effective approach for calculations of absolute stability of proteins using focused dielectric constants

scientific article published on November 2009

Electrostatic Energy and Macromolecular Function ⬇️

scientific article published on January 1, 1991

Electrostatic Origin of the Catalytic Effect of a Supramolecular Host Catalyst ⬇️

scientific article published on November 5, 2012

Electrostatic Origin of the Catalytic Power of Enzymes and the Role of Preorganized Active Sites ⬇️

scientific article published on October 16, 1998

Electrostatic basis for bioenergetics.

scientific article published in January 2004

Electrostatic basis for enzyme catalysis

scientific article

Electrostatic basis for the unidirectionality of the primary proton transfer in cytochrome c oxidase.

scientific article

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

scientific article published in February 2007

Electrostatic contributions to protein stability and folding energy

scientific article published on 20 April 2007

Electrostatic contributions to protein–protein binding affinities: Application to Rap/Raf interaction ⬇️

scientific article published on March 1, 1998

Electrostatic control of GTP and GDP binding in the oncoprotein p21ras

scientific article

Electrostatic control of charge separation in bacterial photosynthesis

scientific article published in June 1990

Electrostatic control of the efficiency of light-induced electron transfer across membranes

scientific article

Electrostatic effects in macromolecules: fundamental concepts and practical modeling ⬇️

scientific article published on April 1, 1998

Electrostatic origin of the mechanochemical rotary mechanism and the catalytic dwell of F1-ATPase ⬇️

scientific article published on December 5, 2011

Electrostatic origin of the unidirectionality of walking myosin V motors

scientific article published on 08 October 2013

Empirical valence bond calculations of enzyme catalysis

scientific article published on 01 January 1981

Energetics of enzyme catalysis ⬇️

scientific article published on November 1, 1978

Energetics of ion permeation through membrane channels. Solvation of Na+ by gramicidin A.

scientific article

Energy considerations show that low-barrier hydrogen bonds do not offer a catalytic advantage over ordinary hydrogen bonds

scientific article

Energy-structure correlation in metalloporphyrins and the control of oxygen binding by hemoglobin

scientific article

Enhancing Paradynamics for QM/MM Sampling of Enzymatic Reactions

scientific article published on 11 February 2016

Enzyme millisecond conformational dynamics do not catalyze the chemical step

scientific article

Enzymes work by solvation substitution rather than by desolvation

scientific article

Equilibrium fluctuation relations for voltage coupling in membrane proteins

scientific article

Evaluation of catalytic free energies in genetically modified proteins

scientific article published on May 1988

Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease

scientific article published on June 2000

Examining the case for the effect of barrier compression on tunneling, vibrationally enhanced catalysis, catalytic entropy and related issues

scientific article

Exploration of the cytochrome c oxidase pathway puzzle and examination of the origin of elusive mutational effects

scientific article

Exploring alternative catalytic mechanisms of the Cas9 HNH domain

scientific article published on 06 September 2019

Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase ⬇️

scientific article published on September 9, 2010

Exploring pathways and barriers for coupled ET/PT in cytochrome c oxidase: a general framework for examining energetics and mechanistic alternatives.

scientific article

Exploring the Catalytic Reaction of Cysteine Proteases

scientific article published on 02 December 2020

Exploring the Dependence of QM/MM Calculations of Enzyme Catalysis on the Size of the QM Region

scientific article published on 23 August 2016

Exploring the Development of Ground-State Destabilization and Transition-State Stabilization in Two Directed Evolution Paths of Kemp Eliminases

scientific article

Exploring the Drug Resistance of HCV Protease

scientific article published on 21 June 2017

Exploring the Effectiveness of Binding Free Energy Calculations

scientific article published on 14 October 2019

Exploring the Mechanism of Covalent Inhibition: Simulating the Binding Free Energy of α-Ketoamide Inhibitors of the Main Protease of SARS-CoV-2

scientific article published on 18 November 2020

Exploring the Proteolysis Mechanism of the Proteasomes

scientific article published on 04 June 2020

Exploring the activation pathway and Gi-coupling specificity of the μ-opioid receptor

scientific article published on 05 October 2020

Exploring the challenges of computational enzyme design by rebuilding the active site of a dehalogenase

scientific article published on 8 January 2019

Exploring the free-energy landscape of GPCR activation

article published in the Proceedings of the National Academy of Sciences of the United States of America

Exploring the mechanism of DNA polymerases by analyzing the effect of mutations of active site acidic groups in Polymerase β

scientific article published on 2 August 2016

Exploring the nature of the translocon-assisted protein insertion ⬇️

scientific article published on December 26, 2012

Exploring the origin of the ion selectivity of the KcsA potassium channel

scientific article published in August 2003

Exploring the role of large conformational changes in the fidelity of DNA polymerase beta

scientific article published on January 2008

Exploring, Refining, and Validating the Paradynamics QM/MM Sampling ⬇️

scientific article published on August 21, 2012

Folding and stability of helical proteins: carp myogen

scientific article published on September 15, 1976

Folding proteins along the dotted lines (reply)

journal article; published in Nature, 1975-04

Free energy of charges in solvated proteins: microscopic calculations using a reversible charging process

scientific article published on 01 December 1986

Frozen Density Functional Free Energy Simulations of Redox Proteins: Computational Studies of the Reduction Potential of Plastocyanin and Rusticyanin ⬇️

scientific article published on April 30, 2003

How do serine proteases really work?

scientific article

How does GAP catalyze the GTPase reaction of Ras? A computer simulation study

scientific article published on August 2000

How important are entropic contributions to enzyme catalysis?

scientific article

How much do enzymes really gain by restraining their reacting fragments?

scientific article published in April 2002

In Defense of Merit in Science

scientific article published on 28 April 2023

Interpretation of resonance Raman spectra of biological molecules ⬇️

scientific article published on January 1, 1977

Inverting the selectivity of aquaporin 6: gating versus direct electrostatic interaction

scientific article

Ketosteroid isomerase provides further support for the idea that enzymes work by electrostatic preorganization

scientific article

Kinetic and spectroscopic effects of protein-chromophore electrostatic interactions in bacteriorhodopsin ⬇️

scientific article published on August 1, 1979

Linear free energy relationships in the intrinsic and GTPase activating protein-stimulated guanosine 5'-triphosphate hydrolysis of p21ras.

scientific article published in November 1996

Macroscopic models for studies of electrostatic interactions in proteins: limitations and applicability

scientific article published on August 1984

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

scientific article published on 3 November 2006

Mechanistic alternatives in phosphate monoester hydrolysis: what conclusions can be drawn from available experimental data?

scientific article

Mechanistic analysis of the observed linear free energy relationships in p21ras and related systems.

scientific article published in November 1996

Methyltransferases do not work by compression, cratic, or desolvation effects, but by electrostatic preorganization

scientific article

Microscopic simulation of quantum dynamics and nuclear tunneling in bacterial reaction centers

scientific article published in January 1989

Misunderstanding the preorganization concept can lead to confusions about the origin of enzyme catalysis

scientific article

Modeling electrostatic effects in proteins

scientific article published on 25 August 2006

Modeling gating charge and voltage changes in response to charge separation in membrane proteins

scientific article

Modifying the beta,gamma leaving-group bridging oxygen alters nucleotide incorporation efficiency, fidelity, and the catalytic mechanism of DNA polymerase beta

scientific article

Molecular dynamics simulations of biological reactions

scientific article (publication date: June 2002)

Monte Carlo simulations of proton pumps: on the working principles of the biological valve that controls proton pumping in cytochrome c oxidase

scientific article

Multiscale Modeling of Biological Functions: From Enzymes to Molecular Machines (Nobel Lecture)

scientific article (publication date: 24 July 2014)

Multiscale modeling of biological functions

scientific article

Multiscale simulations of protein landscapes: using coarse-grained models as reference potentials to full explicit models

scientific article published on April 2010

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

scientific article

On low-barrier hydrogen bonds and enzyme catalysis.

scientific article published in July 1995

On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions

scientific article

On the Origins of the Linear Free Energy Relationships: Exploring the Nature of the Off-Diagonal Coupling Elements in S(N)2 Reactions

scientific article published on 29 March 2012

On the challenge of exploring the evolutionary trajectory from phosphotriesterase to arylesterase using computer simulations

scientific article published on 13 February 2015

On the control of the proton current in the voltage-gated proton channel Hv1

article published in the Proceedings of the National Academy of Sciences of the United States of America

On the energetics of ATP hydrolysis in solution

scientific article published in November 2009

On the energetics of translocon-assisted insertion of charged transmembrane helices into membranes ⬇️

scientific article published on September 27, 2010

On the generation of catalytic antibodies by transition state analogues.

scientific article published in April 2003

On the interpretation of the observed linear free energy relationship in phosphate hydrolysis: a thorough computational study of phosphate diester hydrolysis in solution

scientific article published on 29 February 2008

On the mechanism of guanosine triphosphate hydrolysis in ras p21 proteins

scientific article published on September 22, 1992

On the mechanism of hydrolysis of phosphate monoesters dianions in solutions and proteins

scientific article

On the nature of the apparent free energy of inserting amino acids into membrane through the translocon

scientific article

On the origin of the catalytic power of carboxypeptidase A and other metalloenzymes

scientific article

On the origin of the electrostatic barrier for proton transport in aquaporin

scientific article published in July 2004

On the relationship between folding and chemical landscapes in enzyme catalysis

scholarly article

On the relationship between thermal stability and catalytic power of enzymes

scientific article

On unjustifiably misrepresenting the EVB approach while simultaneously adopting it

scientific article published on August 2009

Origin of the Non-Arrhenius Behavior of the Rates of Enzymatic Reactions.

scientific article published on 14 June 2017

Origin of the temperature dependence of isotope effects in enzymatic reactions: the case of dihydrofolate reductase

scientific article published on 16 June 2007

Paradynamics: an effective and reliable model for ab initio QM/MM free-energy calculations and related tasks

scientific article published on 27 May 2011

Perspective: Defining and quantifying the role of dynamics in enzyme catalysis

scientific article (publication date: 14 May 2016)

Phosphate ester analogues as probes for understanding enzyme catalysed phosphoryl transfer

Polarizable Force Fields:  History, Test Cases, and Prospects

scientific article

Prechemistry barriers and checkpoints do not contribute to fidelity and catalysis as long as they are not rate limiting

article by B. Ram Prasad et al published 23 November 2012 in Theoretical Chemistry Accounts

Prechemistry versus preorganization in DNA replication fidelity ⬇️

scientific article published on August 26, 2011

Predicting drug-resistant mutations of HIV protease

scientific article

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

scientific article published on February 2009

Protein Control of Redox Potentials of Ironminus signSulfur Proteins

scientific article published in November 1996

Protein control of iron-sulfur cluster redox potentials ⬇️

scientific article published on December 25, 1992

Proton-transport mechanisms in cytochrome c oxidase revealed by studies of kinetic isotope effects

scientific article published on 2 April 2011

Q-Chem 2.0: a high-performanceab initio electronic structure program package

scientific article published in 2000

Quantifying free energy profiles of proton transfer reactions in solution and proteins by using a diabatic FDFT mapping

scientific article published in January 2008

Quantifying the mechanism of phosphate monoester hydrolysis in aqueous solution by evaluating the relevant ab initio QM/MM free-energy surfaces

scientific article published on 30 May 2013

Quantitative exploration of the molecular origin of the activation of GTPase

scientific article

Realistic simulation of the activation of voltage-gated ion channels ⬇️

scientific article published on February 13, 2012

Realistic simulations of proton transport along the gramicidin channel: demonstrating the importance of solvation effects

scientific article

Realistic simulations of the coupling between the protomotive force and the mechanical rotation of the F 0 -ATPase ⬇️

scientific article published on August 27, 2012

Reexamining the origin of the directionality of myosin V.

scientific article published on 11 September 2017

Refining the treatment of membrane proteins by coarse-grained models

scientific article published on 4 November 2015

Remarkable rate enhancement of orotidine 5'-monophosphate decarboxylase is due to transition-state stabilization rather than to ground-state destabilization.

scientific article published in December 2000

Renormalizing SMD: The Renormalization Approach and Its Use in Long Time Simulations and Accelerated PMF Calculations of Macromolecules ⬇️

scientific article published on October 7, 2010

Reorganization Energy of the Initial Electron-Transfer Step in Photosynthetic Bacterial Reaction Centers ⬇️

scientific article published on January 1, 1998

Reply to Karplus: Conformational dynamics have no role in the chemical step

article published in the Proceedings of the National Academy of Sciences of the United States of America

Response to Vilfan: Constructing structure-based free energy surfaces is the key to understand myosin V unidirectionality

scientific article published on May 2014

Revisiting the protomotive vectorial motion of F0-ATPase

scientific article published on 11 September 2019

Role of active site residues in the glycosylase step of T4 endonuclease V. Computer simulation studies on ionization states

scientific article published in July 1999

Role of arginine-38 in regulation of the cytochrome c oxidation-reduction equilibrium

scientific article published on 01 April 1989

Role of the chlorophyll dimer in bacterial photosynthesis

scientific article

Semiquantitative calculations of catalytic free energies in genetically modified enzymes

scientific article published on 01 May 1987

Simulating electrostatic energies in proteins: perspectives and some recent studies of pKas, redox, and other crucial functional properties.

scientific article

Simulating large nuclear quantum mechanical corrections in hydrogen atom transfer reactions in metalloenzymes

scientific article published on 9 December 2003

Simulating proton translocations in proteins: probing proton transfer pathways in the Rhodobacter sphaeroides reaction center

scientific article published on September 1999

Simulating redox coupled proton transfer in cytochrome c oxidase: looking for the proton bottleneck.

scientific article published in April 2005

Simulating the Function of the MjNhaP1 Transporter

scientific article published on 21 September 2016

Simulating the catalytic effect of a designed mononuclear zinc metalloenzyme that catalyzes the hydrolysis of phosphate triesters

scientific article published on 13 October 2014

Simulating the dynamics of the mechanochemical cycle of myosin-V.

scientific article published on 13 February 2017

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

scientific article published on June 2006

Simulating the electrostatic guidance of the vectorial translocations in hexameric helicases and translocases

scientific article

Simulating the fidelity and the three Mg mechanism of pol η and clarifying the validity of transition state theory in enzyme catalysis

scientific article published on 6 April 2017

Simulating the function of sodium/proton antiporters

scientific article

Simulating the pulling of stalled elongated peptide from the ribosome by the translocon ⬇️

scientific article published on May 31, 2013

Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches

Simulation of tunneling in enzyme catalysis by combining a biased propagation approach and the quantum classical path method: application to lipoxygenase

scientific article published on 11 December 2007

Simulations of ion current in realistic models of ion channels: the KcsA potassium channel

scientific article published in May 2002

Simulations of the large kinetic isotope effect and the temperature dependence of the hydrogen atom transfer in lipoxygenase

scientific article (publication date: 10 March 2004)

Solute solvent dynamics and energetics in enzyme catalysis: the S(N)2 reaction of dehalogenase as a general benchmark.

scientific article published in November 2004

Solvation free energies of molecules. The most stable anionic tautomers of uracil

scientific article

Structure/function correlations of proteins using MM, QM/MM, and related approaches: methods, concepts, pitfalls, and current progress

scientific article published on January 2003

Studies of proton translocations in biological systems: simulating proton transport in carbonic anhydrase by EVB-based models

scientific article

Substrate-assisted catalysis as a mechanism for GTP hydrolysis of p21ras and other GTP-binding proteins.

scientific article published in January 1995

The EVB as a quantitative tool for formulating simulations and analyzing biological and chemical reactions

scientific article published on January 2010

The Effect of Protein Relaxation on Charge-Charge Interactions and Dielectric Constants of Proteins ⬇️

scientific article published on April 1, 1998

The Empirical Valence Bond (EVB) Method

The FOF1 ATP synthase: from atomistic three-dimensional structure to the rotary-chemical function

scientific article published on 3 July 2017

The Physics and Physical Chemistry of Molecular Machines

scientific article

The barrier for proton transport in aquaporins as a challenge for electrostatic models: the role of protein relaxation in mutational calculations

scientific article published on September 2006

The catalytic dwell in ATPases is not crucial for movement against applied torque

scientific article published on 21 September 2020

The catalytic effect of dihydrofolate reductase and its mutants is determined by reorganization energies

scientific article published in May 2007

The control of the discrimination between dNTP and rNTP in DNA and RNA polymerase

scientific article published on 2 August 2016

The empirical valence bond as an effective strategy for computer-aided enzyme design

scientific article published on April 2009

The empirical valence bond model: theory and applications

article

The energetics of the primary proton transfer in bacteriorhodopsin revisited: it is a sequential light-induced charge separation after all

scientific article published on 14 March 2008

The entropic contributions in vitamin B12 enzymes still reflect the electrostatic paradigm

scientific article

The low barrier hydrogen bond (LBHB) proposal revisited: the case of the Asp... His pair in serine proteases

scientific article published in May 2004

Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme

scientific article published on May 15, 1976

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

scientific article published on October 2005

Torque, chemistry and efficiency in molecular motors: a study of the rotary-chemical coupling in F1-ATPase

scientific article

Toward accurate microscopic calculation of solvation entropies: extending the restraint release approach to studies of solvation effects

scientific article

Toward accurate screening in computer-aided enzyme design

scientific article

Toward computer-aided site-directed mutagenesis of enzymes

scientific article published on June 1986

Towards Quantitative Computer‐Aided Studies of Enzymatic Enantioselectivity: The Case of Candida antarctica Lipase A ⬇️

scientific article published on December 21, 2011

Towards accurate ab initio QM/MM calculations of free-energy profiles of enzymatic reactions

scientific article

Transition state theory can be used in studies of enzyme catalysis: lessons from simulations of tunnelling and dynamical effects in lipoxygenase and other systems

scientific article

Using a charging coordinate in studies of ionization induced partial unfolding

scientific article

Using the constrained DFT approach in generating diabatic surfaces and off diagonal empirical valence bond terms for modeling reactions in condensed phases

scientific article published in October 2006

Validating a Coarse-Grained Voltage Activation Model by Comparing Its Performance to the Results of Monte Carlo Simulations.

scientific article

Validating computer simulations of enantioselective catalysis; reproducing the large steric and entropic contributions in Candida Antarctica lipase B

scientific article

Validating the Water Flooding Approach by Comparing It to Grand Canonical Monte Carlo Simulations

scientific article published on 14 September 2017

Validating the vitality strategy for fighting drug resistance ⬇️

scientific article published on January 31, 2012

What about protein polarity?

scientific article published in Nature

What are the dielectric "constants" of proteins and how to validate electrostatic models?

scientific article

What are the roles of substrate-assisted catalysis and proximity effects in peptide bond formation by the ribosome?

scientific article published in August 2005

What really prevents proton transport through aquaporin? Charge self-energy versus proton wire proposals

scientific article

Why does the Ras switch "break" by oncogenic mutations?

scientific article

Why have mutagenesis studies not located the general base in ras p21 ⬇️

scientific article published on July 1, 1994

Why ion pair reversal by protein engineering is unlikely to succeed

scientific article published in Nature

Why nature really chose phosphate

scientific article published on 15 January 2013

ZnT2 is an electroneutral proton-coupled vesicular antiporter displaying an apparent stoichiometry of two protons per zinc ion

scientific article published on 20 March 2019

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