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Lista de obras de Arieh Warshel

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

artículo científico publicado en 2015

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

artículo científico publicado en 2010

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

artículo científico publicado en 2010

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

artículo científico publicado en 2009

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

artículo científico publicado el 1 de diciembre de 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

artículo científico publicado en 2007

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

artículo científico publicado el 1 de enero de 1996

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

artículo científico publicado en 2010

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

artículo científico publicado en 2012

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

artículo científico publicado en 2006

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

artículo científico publicado en 2010

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

artículo científico publicado en 2014

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

artículo científico publicado en 2003

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

artículo científico publicado en 2009

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

artículo científico publicado en 2008

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

artículo científico publicado en 2010

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

artículo científico publicado el 22 de abril de 1976

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

artículo científico publicado en 2015

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

artículo científico publicado en 1974

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.

artículo científico publicado en 1994

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

artículo científico publicado el 1 de abril de 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 ⬇️

artículo científico publicado el 1 de agosto de 1984

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

artículo científico publicado en 1981

Calculations of free energy profiles for the staphylococcal nuclease catalyzed reaction

artículo científico publicado en 1989

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

artículo científico publicado en 2012

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

artículo científico publicado en 2011

Catalytic effects of mutations of distant protein residues in human DNA polymerase β: theory and experiment

scientific article published on 29 October 2012

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

artículo científico publicado el 15 de abril de 2011

Charge stabilization mechanism in the visual and purple membrane pigments ⬇️

artículo científico publicado el 1 de junio de 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

artículo científico publicado en 1993

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

artículo científico publicado en 2001

Coarse grained model for exploring voltage dependent ion channels ⬇️

artículo científico publicado el 5 de agosto de 2011

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

artículo científico publicado en 2011

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

artículo científico publicado en 2014

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

artículo científico publicado en 2000

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

artículo científico publicado el 1 de enero de 1991

Computer aided enzyme design and catalytic concepts

artículo científico publicado en 2014

Computer simulation of protein folding

artículo científico publicado el 27 de febrero de 1975

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

artículo científico publicado en 2003

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

artículo científico publicado el 5 de marzo de 1992

Computer simulation studies of the fidelity of DNA polymerases

artículo científico publicado en 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

artículo científico publicado el 1 de enero de 1992

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

artículo científico publicado en 1998

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

artículo científico publicado en 2003

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

artículo científico publicado en 2005

Conformation of retinal isomers

artículo científico publicado en 1974

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

artículo científico publicado en 1970

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

artículo científico publicado en 1968

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

artículo científico publicado en 1970

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

artículo científico publicado en 1986

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

artículo científico publicado el 1 de agosto de 1979

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

artículo científico publicado en 2003

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

artículo científico publicado el 15 de agosto de 1983

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

artículo científico publicado el 26 de mayo de 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

artículo científico publicado en 2007

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

artículo científico publicado en 2007

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

artículo científico publicado en 2018

Dineopentyl phosphate hydrolysis: evidence for stepwise water attack

artículo científico publicado en 2008

Dipoles localized at helix termini of proteins stabilize charges

artículo científico publicado en 1991

Dispersed polaron simulations of electron transfer in photosynthetic reaction centers

artículo científico publicado en 1989

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

artículo científico publicado en 2015

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

artículo científico publicado en 2006

Dynamics of biochemical and biophysical reactions: insight from computer simulations

artículo científico publicado en 2001

Dynamics of enzymatic reactions

artículo científico publicado en 1984

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

artículo científico publicado el 5 de abril de 1992

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

artículo científico publicado en 2009

Electrostatic Energy and Macromolecular Function ⬇️

artículo científico publicado el 1 de enero de 1991

Electrostatic basis for bioenergetics.

artículo científico publicado en 2004

Electrostatic basis for enzyme catalysis

artículo científico publicado en 2006

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

artículo científico publicado en 2008

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

artículo científico publicado en 2007

Electrostatic contributions to protein stability and folding energy

artículo científico publicado en 2007

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

artículo científico publicado el 1 de marzo de 1998

Electrostatic control of GTP and GDP binding in the oncoprotein p21ras

artículo científico publicado en 1996

Electrostatic control of charge separation in bacterial photosynthesis

artículo científico publicado en 1990

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

artículo científico publicado en 1981

Electrostatic effects in macromolecules: fundamental concepts and practical modeling

artículo científico publicado en 1998

Electrostatic origin of the catalytic effect of a supramolecular host catalyst

artículo científico publicado en 2012

Electrostatic origin of the catalytic power of enzymes and the role of preorganized active sites

artículo científico publicado en 1998

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

artículo científico publicado el 5 de diciembre de 2011

Electrostatic origin of the unidirectionality of walking myosin V motors

artículo científico publicado en 2013

Empirical valence bond calculations of enzyme catalysis

scientific article published on 01 January 1981

Energetics of enzyme catalysis ⬇️

artículo científico publicado el 1 de noviembre de 1978

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

artículo científico publicado en 1989

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

artículo científico publicado en 1996

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

artículo científico publicado en 1977

Enhancing Paradynamics for QM/MM Sampling of Enzymatic Reactions

artículo científico publicado en 2016

Enzyme millisecond conformational dynamics do not catalyze the chemical step

artículo científico publicado en 2009

Enzymes work by solvation substitution rather than by desolvation

artículo científico publicado en 1989

Equilibrium fluctuation relations for voltage coupling in membrane proteins

artículo científico publicado en 2015

Evaluation of catalytic free energies in genetically modified proteins

artículo científico publicado en 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

artículo científico publicado en 2000

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

artículo científico publicado en 2010

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

artículo científico publicado en 2011

Exploring alternative catalytic mechanisms of the Cas9 HNH domain

artículo científico publicado en 2019

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

artículo científico publicado el 9 de septiembre de 2010

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

artículo científico publicado en 2007

Exploring the Catalytic Reaction of Cysteine Proteases

artículo científico publicado en 2020

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

artículo científico publicado en 2016

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

artículo científico publicado en 2017

Exploring the Drug Resistance of HCV Protease

artículo científico publicado en 2017

Exploring the Effectiveness of Binding Free Energy Calculations

artículo científico publicado en 2019

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

artículo científico publicado en 2020

Exploring the Proteolysis Mechanism of the Proteasomes

artículo científico publicado en 2020

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

artículo científico publicado en 2020

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

artículo científico publicado en 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

artículo científico publicado en 2016

Exploring the nature of the translocon-assisted protein insertion

artículo científico publicado en 2012

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

artículo científico publicado en 2003

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

artículo científico publicado en 2008

Exploring, refining, and validating the paradynamics QM/MM sampling

artículo científico

Folding and stability of helical proteins: carp myogen

artículo científico publicado el 15 de septiembre de 1976

Folding proteins along the dotted lines (reply)

artículo científico publicado en 1975

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

artículo científico publicado en 1986

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

artículo científico publicado el 30 de abril de 2003

How do serine proteases really work?

artículo científico publicado en 1989

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

artículo científico publicado en 2000

How important are entropic contributions to enzyme catalysis?

artículo científico publicado en 2000

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

artículo científico publicado en 2002

Interpretation of resonance Raman spectra of biological molecules ⬇️

artículo científico publicado el 1 de enero de 1977

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

artículo científico publicado en 2005

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

artículo científico publicado en 2010

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

artículo científico publicado el 1 de agosto de 1979

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

artículo científico publicado en 1996

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

artículo científico publicado en 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

artículo científico publicado en 2006

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

artículo científico publicado en 1999

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

artículo científico publicado en 1996

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

artículo científico publicado en 2015

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

artículo científico publicado en 1989

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

artículo científico publicado en 2017

Modeling electrostatic effects in proteins

artículo científico publicado en 2006

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

artículo científico publicado en 2014

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

artículo científico publicado en 2007

Molecular dynamics simulations of biological reactions

artículo científico publicado en 2002

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

artículo científico publicado en 2006

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

artículo científico publicado en 2014

Multiscale modeling of biological functions

artículo científico publicado en 2011

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

artículo científico publicado en 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

artículo científico publicado en 2010

On low-barrier hydrogen bonds and enzyme catalysis.

artículo científico publicado en 1995

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

artículo científico publicado en 2005

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

artículo científico publicado en 2012

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

artículo científico publicado en 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

artículo científico publicado en 2009

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

artículo científico publicado el 27 de septiembre de 2010

On the generation of catalytic antibodies by transition state analogues.

artículo científico publicado en 2003

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

artículo científico publicado en 2008

On the mechanism of guanosine triphosphate hydrolysis in ras p21 proteins

artículo científico publicado el 22 de septiembre de 1992

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

artículo científico publicado en 2006

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

artículo científico publicado en 2013

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

artículo científico publicado en 2009

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

artículo científico publicado en 2004

On the relationship between folding and chemical landscapes in enzyme catalysis

artículo científico publicado en 2008

On the relationship between thermal stability and catalytic power of enzymes

artículo científico publicado en 2007

On unjustifiably misrepresenting the EVB approach while simultaneously adopting it

artículo científico publicado en 2009

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

artículo científico publicado en 2017

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

artículo científico publicado en 2007

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

artículo científico publicado en 2011

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

artículo científico publicado en 2016

Phosphate ester analogues as probes for understanding enzyme catalysed phosphoryl transfer

Polarizable Force Fields:  History, Test Cases, and Prospects

artículo científico publicado en 2007

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 ⬇️

artículo científico publicado el 26 de agosto de 2011

Predicting drug-resistant mutations of HIV protease

artículo científico publicado en 2008

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

artículo científico publicado en 2009

Protein Control of Redox Potentials of Ironminus signSulfur Proteins

artículo científico publicado en 1996

Protein control of iron-sulfur cluster redox potentials ⬇️

artículo científico publicado el 25 de diciembre de 1992

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

artículo científico publicado en 2011

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

artículo científico publicado en 2000

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

artículo científico publicado en 2008

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

artículo científico publicado en 2013

Quantitative exploration of the molecular origin of the activation of GTPase

artículo científico publicado en 2013

Realistic simulation of the activation of voltage-gated ion channels

artículo científico publicado en 2012

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

artículo científico publicado en 2005

Realistic simulations of the coupling between the protomotive force and the mechanical rotation of the F0-ATPase

artículo científico publicado en 2012

Reexamining the origin of the directionality of myosin V.

artículo científico publicado en 2017

Refining the treatment of membrane proteins by coarse-grained models

artículo científico publicado en 2015

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

artículo científico publicado en 2000

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

artículo científico publicado el 7 de octubre de 2010

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

artículo científico publicado el 1 de enero de 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

artículo científico publicado en 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

artículo científico publicado en 1999

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

artículo científico publicado en 1989

Role of the chlorophyll dimer in bacterial photosynthesis

artículo científico publicado en 1980

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.

artículo científico publicado en 2011

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

artículo científico publicado en 2003

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

artículo científico publicado en 1999

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

artículo científico publicado en 2005

Simulating the Function of the MjNhaP1 Transporter

artículo científico publicado en 2016

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

artículo científico publicado en 2014

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

artículo científico publicado en 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

artículo científico publicado en 2006

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

artículo científico publicado en 2009

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

artículo científico publicado en 2017

Simulating the function of sodium/proton antiporters

artículo científico publicado en 2015

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

artículo científico publicado en 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

artículo científico publicado en 2002

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

artículo científico publicado en 2004

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

artículo científico publicado en 2004

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

artículo científico publicado en 2008

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

artículo científico publicado en 2003

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

artículo científico publicado en 2004

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

artículo científico publicado en 1995

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

artículo científico publicado en 2010

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

artículo científico publicado el 1 de abril de 1998

The Empirical Valence Bond (EVB) Method

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

artículo científico publicado en 2017

The Physics and Physical Chemistry of Molecular Machines

artículo científico publicado en 2016

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

artículo científico publicado en 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

artículo científico publicado en 2007

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

artículo científico publicado en 2016

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

artículo científico publicado en 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

artículo científico publicado en 2008

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

artículo científico publicado en 2015

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

artículo científico publicado en 2004

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

artículo científico publicado el 15 de mayo de 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

artículo científico publicado en 2005

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

artículo científico publicado en 2015

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

artículo científico publicado en 2009

Toward accurate screening in computer-aided enzyme design

artículo científico publicado en 2009

Toward computer-aided site-directed mutagenesis of enzymes

artículo científico publicado en 1986

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

artículo científico publicado en 2006

Towards quantitative computer-aided studies of enzymatic enantioselectivity: the case of Candida antarctica lipase A.

artículo científico publicado en 2011

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

artículo científico publicado en 2006

Using a charging coordinate in studies of ionization induced partial unfolding

artículo científico publicado en 2006

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

artículo científico publicado en 2006

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

artículo científico publicado en 2017

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

artículo científico publicado en 2014

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

artículo científico publicado en 2017

Validating the vitality strategy for fighting drug resistance ⬇️

artículo científico publicado en 2012

What about protein polarity?

artículo científico publicado en 1987

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

artículo científico publicado en 2001

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

artículo científico publicado en 2005

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

artículo científico publicado en 2003

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

artículo científico publicado en 2004

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

artículo científico publicado el 1 de julio de 1994

Why ion pair reversal by protein engineering is unlikely to succeed

scientific article published in Nature

Why nature really chose phosphate

artículo científico

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

artículo científico publicado en 2019

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