Published in J Phys Chem B on January 13, 2005
Multiscale simulations of protein landscapes: using coarse-grained models as reference potentials to full explicit models. Proteins (2010) 1.36
Electrostatic basis for the unidirectionality of the primary proton transfer in cytochrome c oxidase. Proc Natl Acad Sci U S A (2008) 1.27
Water wires in atomistic models of the Hv1 proton channel. Biochim Biophys Acta (2011) 1.07
Temperature dependence of proton permeation through a voltage-gated proton channel. J Gen Physiol (2009) 1.05
Toward theoretical analysis of long-range proton transfer kinetics in biomolecular pumps. J Phys Chem A (2006) 1.04
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. J Phys Chem B (2005) 1.01
Charge delocalization in proton channels, II: the synthetic LS2 channel and proton selectivity. Biophys J (2006) 0.93
Realistic simulations of the coupling between the protomotive force and the mechanical rotation of the F0-ATPase. Proc Natl Acad Sci U S A (2012) 0.93
Quantum dynamics in continuum for proton transport II: Variational solvent-solute interface. Int J Numer Method Biomed Eng (2011) 0.91
Ion conductance vs. pore gating and selectivity in KcsA channel: modeling achievements and perspectives. J Mol Model (2007) 0.87
Quantum dynamics in continuum for proton transport--generalized correlation. J Chem Phys (2012) 0.83
Functional role of Asp160 and the deprotonation mechanism of ammonium in the Escherichia coli ammonia channel protein AmtB. J Phys Chem B (2009) 0.81
Quantum Dynamics in Continuum for Proton Transport I: Basic Formulation. Commun Comput Phys (2012) 0.81
Multiscale modeling of biological functions. Phys Chem Chem Phys (2011) 0.81
Ultrafast proton transport in sub-1-nm diameter carbon nanotube porins. Nat Nanotechnol (2016) 0.77
Modeling negative ion defect migration through the gramicidin A channel. J Mol Model (2009) 0.75
Advances in methods and algorithms in a modern quantum chemistry program package. Phys Chem Chem Phys (2006) 6.51
At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis? Proteins (2010) 2.69
Dynamical contributions to enzyme catalysis: critical tests of a popular hypothesis. Chem Rev (2006) 2.10
Enzyme millisecond conformational dynamics do not catalyze the chemical step. Proc Natl Acad Sci U S A (2009) 2.08
Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions. Proc Natl Acad Sci U S A (2011) 1.94
Origin of the temperature dependence of isotope effects in enzymatic reactions: the case of dihydrofolate reductase. J Phys Chem B (2007) 1.77
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. J Phys Chem B (2009) 1.66
DNA polymerase beta fidelity: halomethylene-modified leaving groups in pre-steady-state kinetic analysis reveal differences at the chemical transition state. Biochemistry (2007) 1.61
Modifying the beta,gamma leaving-group bridging oxygen alters nucleotide incorporation efficiency, fidelity, and the catalytic mechanism of DNA polymerase beta. Biochemistry (2007) 1.61
Computer simulation of the chemical catalysis of DNA polymerases: discriminating between alternative nucleotide insertion mechanisms for T7 DNA polymerase. J Am Chem Soc (2003) 1.58
Computer simulations of protein functions: searching for the molecular origin of the replication fidelity of DNA polymerases. Proc Natl Acad Sci U S A (2005) 1.58
The catalytic effect of dihydrofolate reductase and its mutants is determined by reorganization energies. Biochemistry (2007) 1.57
What really prevents proton transport through aquaporin? Charge self-energy versus proton wire proposals. Biophys J (2003) 1.53
Predicting clinical physiology: a Markov chain model of heart rate recovery after spontaneous breathing trials in mechanically ventilated patients. J Crit Care (2009) 1.50
The barrier for proton transport in aquaporins as a challenge for electrostatic models: the role of protein relaxation in mutational calculations. Proteins (2006) 1.49
On the mechanism of hydrolysis of phosphate monoesters dianions in solutions and proteins. J Am Chem Soc (2006) 1.48
Simulations of the large kinetic isotope effect and the temperature dependence of the hydrogen atom transfer in lipoxygenase. J Am Chem Soc (2004) 1.46
Why nature really chose phosphate. Q Rev Biophys (2013) 1.46
Absolute binding free energy calculations: on the accuracy of computational scoring of protein-ligand interactions. Proteins (2010) 1.45
On the relationship between folding and chemical landscapes in enzyme catalysis. Proc Natl Acad Sci U S A (2008) 1.44
Converting conformational changes to electrostatic energy in molecular motors: The energetics of ATP synthase. Proc Natl Acad Sci U S A (2003) 1.44
Exploring the origin of the ion selectivity of the KcsA potassium channel. Proteins (2003) 1.43
Why does the Ras switch "break" by oncogenic mutations? Proteins (2004) 1.39
On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions. J Phys Chem B (2005) 1.37
Multiscale simulations of protein landscapes: using coarse-grained models as reference potentials to full explicit models. Proteins (2010) 1.36
On the interpretation of the observed linear free energy relationship in phosphate hydrolysis: a thorough computational study of phosphate diester hydrolysis in solution. Biochemistry (2008) 1.34
Electrostatic origin of the mechanochemical rotary mechanism and the catalytic dwell of F1-ATPase. Proc Natl Acad Sci U S A (2011) 1.33
Apparent NAC effect in chorismate mutase reflects electrostatic transition state stabilization. J Am Chem Soc (2003) 1.33
Monte Carlo simulations of proton pumps: on the working principles of the biological valve that controls proton pumping in cytochrome c oxidase. Proc Natl Acad Sci U S A (2006) 1.32
Coarse-grained (multiscale) simulations in studies of biophysical and chemical systems. Annu Rev Phys Chem (2011) 1.30
Using a charging coordinate in studies of ionization induced partial unfolding. J Phys Chem B (2006) 1.30
Frozen density functional free energy simulations of redox proteins: computational studies of the reduction potential of plastocyanin and rusticyanin. J Am Chem Soc (2003) 1.30
Exploring the role of large conformational changes in the fidelity of DNA polymerase beta. Proteins (2008) 1.29
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. Biochemistry (2006) 1.28
Studies of proton translocations in biological systems: simulating proton transport in carbonic anhydrase by EVB-based models. Biophys J (2004) 1.28
Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase. Proc Natl Acad Sci U S A (2010) 1.27
Electrostatic basis for the unidirectionality of the primary proton transfer in cytochrome c oxidase. Proc Natl Acad Sci U S A (2008) 1.27
Towards accurate ab initio QM/MM calculations of free-energy profiles of enzymatic reactions. J Phys Chem B (2006) 1.24
On the energetics of translocon-assisted insertion of charged transmembrane helices into membranes. Proc Natl Acad Sci U S A (2010) 1.24
Electrostatic origin of the unidirectionality of walking myosin V motors. Proc Natl Acad Sci U S A (2013) 1.24
Ketosteroid isomerase provides further support for the idea that enzymes work by electrostatic preorganization. Proc Natl Acad Sci U S A (2010) 1.23
What are the roles of substrate-assisted catalysis and proximity effects in peptide bond formation by the ribosome? Biochemistry (2005) 1.23
Plasticity of the systemic inflammatory response to acute infection during critical illness: development of the riboleukogram. PLoS One (2008) 1.19
Simulating redox coupled proton transfer in cytochrome c oxidase: looking for the proton bottleneck. FEBS Lett (2005) 1.18
Converting structural information into an allosteric-energy-based picture for elongation factor Tu activation by the ribosome. Proc Natl Acad Sci U S A (2011) 1.18
The low barrier hydrogen bond (LBHB) proposal revisited: the case of the Asp... His pair in serine proteases. Proteins (2004) 1.17
On the origin of the electrostatic barrier for proton transport in aquaporin. FEBS Lett (2004) 1.15
Solute solvent dynamics and energetics in enzyme catalysis: the S(N)2 reaction of dehalogenase as a general benchmark. J Am Chem Soc (2004) 1.14
Simulating the electrostatic guidance of the vectorial translocations in hexameric helicases and translocases. Proc Natl Acad Sci U S A (2009) 1.13
On the relationship between thermal stability and catalytic power of enzymes. Biochemistry (2007) 1.13
Computer simulation studies of the fidelity of DNA polymerases. Biopolymers (2003) 1.11
Predicting drug-resistant mutations of HIV protease. Angew Chem Int Ed Engl (2008) 1.10
A new paradigm for electrostatic catalysis of radical reactions in vitamin B12 enzymes. Proc Natl Acad Sci U S A (2007) 1.10
Toward accurate screening in computer-aided enzyme design. Biochemistry (2009) 1.06
Effective approach for calculations of absolute stability of proteins using focused dielectric constants. Proteins (2009) 1.04
Coarse grained model for exploring voltage dependent ion channels. Biochim Biophys Acta (2011) 1.02
Prechemistry versus preorganization in DNA replication fidelity. Proteins (2011) 1.02
A comprehensive examination of the contributions to the binding entropy of protein-ligand complexes. Proteins (2010) 1.02
Associative versus dissociative mechanisms of phosphate monoester hydrolysis: on the interpretation of activation entropies. Chemphyschem (2008) 1.02
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. J Mol Biol (2006) 1.02
Realistic simulation of the activation of voltage-gated ion channels. Proc Natl Acad Sci U S A (2012) 1.02
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. J Phys Chem B (2005) 1.01
Paradynamics: an effective and reliable model for ab initio QM/MM free-energy calculations and related tasks. J Phys Chem B (2011) 1.01
Exploring, refining, and validating the paradynamics QM/MM sampling. J Phys Chem B (2012) 1.00
Exploring pathways and barriers for coupled ET/PT in cytochrome c oxidase: a general framework for examining energetics and mechanistic alternatives. Biochim Biophys Acta (2007) 0.99
Transition state theory can be used in studies of enzyme catalysis: lessons from simulations of tunnelling and dynamical effects in lipoxygenase and other systems. Philos Trans R Soc Lond B Biol Sci (2006) 0.99
Are mixed explicit/implicit solvation models reliable for studying phosphate hydrolysis? A comparative study of continuum, explicit and mixed solvation models. Chemphyschem (2009) 0.98
Exploration of the cytochrome c oxidase pathway puzzle and examination of the origin of elusive mutational effects. Biochim Biophys Acta (2011) 0.98
Electrostatic contributions to protein stability and folding energy. FEBS Lett (2007) 0.97
Exploring the nature of the translocon-assisted protein insertion. Proc Natl Acad Sci U S A (2012) 0.97
Renormalizing SMD: the renormalization approach and its use in long time simulations and accelerated PMF calculations of macromolecules. J Phys Chem B (2010) 0.96
The energetics of the primary proton transfer in bacteriorhodopsin revisited: it is a sequential light-induced charge separation after all. Biochim Biophys Acta (2008) 0.96
Simulating large nuclear quantum mechanical corrections in hydrogen atom transfer reactions in metalloenzymes. J Biol Inorg Chem (2003) 0.95
Using the constrained DFT approach in generating diabatic surfaces and off diagonal empirical valence bond terms for modeling reactions in condensed phases. J Phys Chem B (2006) 0.95
Methyltransferases do not work by compression, cratic, or desolvation effects, but by electrostatic preorganization. Proteins (2015) 0.95
Quantifying the mechanism of phosphate monoester hydrolysis in aqueous solution by evaluating the relevant ab initio QM/MM free-energy surfaces. J Phys Chem B (2013) 0.95
On the energetics of ATP hydrolysis in solution. J Phys Chem B (2009) 0.95
An effective coarse-grained model for biological simulations: recent refinements and validations. Proteins (2014) 0.95
Simulating the pulling of stalled elongated peptide from the ribosome by the translocon. Proc Natl Acad Sci U S A (2013) 0.94
Accelerating QM/MM free energy calculations: representing the surroundings by an updated mean charge distribution. J Phys Chem B (2008) 0.94
Towards quantitative computer-aided studies of enzymatic enantioselectivity: the case of Candida antarctica lipase A. Chembiochem (2011) 0.94
Dineopentyl phosphate hydrolysis: evidence for stepwise water attack. J Org Chem (2008) 0.93
Realistic simulations of the coupling between the protomotive force and the mechanical rotation of the F0-ATPase. Proc Natl Acad Sci U S A (2012) 0.93
Addressing open questions about phosphate hydrolysis pathways by careful free energy mapping. J Phys Chem B (2012) 0.92
Quantifying free energy profiles of proton transfer reactions in solution and proteins by using a diabatic FDFT mapping. J Phys Chem B (2008) 0.92
DNA polymerase beta catalytic efficiency mirrors the Asn279-dCTP H-bonding strength. FEBS Lett (2007) 0.92
Challenges and advances in validating enzyme design proposals: the case of kemp eliminase catalysis. Biochemistry (2011) 0.92
Quantitative exploration of the molecular origin of the activation of GTPase. Proc Natl Acad Sci U S A (2013) 0.91
Capturing the energetics of water insertion in biological systems: the water flooding approach. Proteins (2012) 0.89
Dynamical density delay maps: simple, new method for visualising the behaviour of complex systems. BMC Med Inform Decis Mak (2014) 0.89
On unjustifiably misrepresenting the EVB approach while simultaneously adopting it. J Phys Chem B (2009) 0.89
Electrostatic basis for bioenergetics. Methods Enzymol (2004) 0.88
An Analysis of All the Relevant Facts and Arguments Indicates that Enzyme Catalysis Does Not Involve Large Contributions from Nuclear Tunneling. J Phys Org Chem (2010) 0.87
Coarse-grained simulations of the gating current in the voltage-activated Kv1.2 channel. Proc Natl Acad Sci U S A (2014) 0.87
Using systems biology to simplify complex disease: immune cartography. Crit Care Med (2009) 0.86
Simulation of tunneling in enzyme catalysis by combining a biased propagation approach and the quantum classical path method: application to lipoxygenase. J Phys Chem B (2007) 0.86
A binding free energy decomposition approach for accurate calculations of the fidelity of DNA polymerases. Proteins (2010) 0.85
The empirical valence bond as an effective strategy for computer-aided enzyme design. Biotechnol J (2009) 0.84
Proton-transport mechanisms in cytochrome c oxidase revealed by studies of kinetic isotope effects. Biochim Biophys Acta (2011) 0.84
Toward accurate microscopic calculation of solvation entropies: extending the restraint release approach to studies of solvation effects. J Phys Chem B (2009) 0.84