Published in Proc Natl Acad Sci U S A on August 15, 2007
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An electrostatic network and long-range regulation of Src kinases. Protein Sci (2008) 1.30
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Locking the active conformation of c-Src kinase through the phosphorylation of the activation loop. J Mol Biol (2013) 0.98
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Interaction with the Src homology (SH3-SH2) region of the Src-family kinase Hck structures the HIV-1 Nef dimer for kinase activation and effector recruitment. J Biol Chem (2014) 0.83
The feasibility of parameterizing four-state equilibria using relaxation dispersion measurements. J Biomol NMR (2011) 0.81
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An examination of dynamics crosstalk between SH2 and SH3 domains by hydrogen/deuterium exchange and mass spectrometry. Protein Sci (2005) 1.17
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Molecular determinants of gating at the potassium-channel selectivity filter. Nat Struct Mol Biol (2006) 4.64
Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands. Nature (2004) 4.37
Closing in on the resting state of the Shaker K(+) channel. Neuron (2007) 3.49
Calculation of absolute protein-ligand binding free energy from computer simulations. Proc Natl Acad Sci U S A (2005) 3.21
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Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials. Biophys J (2006) 2.88
Two atomic constraints unambiguously position the S4 segment relative to S1 and S2 segments in the closed state of Shaker K channel. Proc Natl Acad Sci U S A (2007) 2.85
Computations of standard binding free energies with molecular dynamics simulations. J Phys Chem B (2009) 2.80
Importance of hydration and dynamics on the selectivity of the KcsA and NaK channels. J Gen Physiol (2007) 2.79
Energetics of ion conduction through the gramicidin channel. Proc Natl Acad Sci U S A (2003) 2.67
Structural basis for the coupling between activation and inactivation gates in K(+) channels. Nature (2010) 2.63
Ion permeation and selectivity of OmpF porin: a theoretical study based on molecular dynamics, Brownian dynamics, and continuum electrodiffusion theory. J Mol Biol (2002) 2.61
Molecular driving forces determining potassium channel slow inactivation. Nat Struct Mol Biol (2007) 2.56
A gate in the selectivity filter of potassium channels. Structure (2005) 2.50
The free energy landscapes governing conformational changes in a glutamate receptor ligand-binding domain. Structure (2007) 2.45
Ion selectivity in potassium channels. Biophys Chem (2006) 2.28
Control of ion selectivity in LeuT: two Na+ binding sites with two different mechanisms. J Mol Biol (2008) 2.27
A microscopic view of ion conduction through the K+ channel. Proc Natl Acad Sci U S A (2003) 2.24
Ions and counterions in a biological channel: a molecular dynamics simulation of OmpF porin from Escherichia coli in an explicit membrane with 1 M KCl aqueous salt solution. J Mol Biol (2002) 2.23
Finding transition pathways using the string method with swarms of trajectories. J Phys Chem B (2008) 2.17
Absolute hydration free energy scale for alkali and halide ions established from simulations with a polarizable force field. J Phys Chem B (2006) 2.15
The hidden energetics of ligand binding and activation in a glutamate receptor. Nat Struct Mol Biol (2011) 2.10
Dynamics of the Kv1.2 voltage-gated K+ channel in a membrane environment. Biophys J (2007) 2.10
Modeling the structure of agitoxin in complex with the Shaker K+ channel: a computational approach based on experimental distance restraints extracted from thermodynamic mutant cycles. Biophys J (2002) 1.98
Molecular mechanism of H+ conduction in the single-file water chain of the gramicidin channel. Biophys J (2002) 1.94
Ion permeation through the alpha-hemolysin channel: theoretical studies based on Brownian dynamics and Poisson-Nernst-Plank electrodiffusion theory. Biophys J (2004) 1.91
Calculation of the gating charge for the Kv1.2 voltage-activated potassium channel. Biophys J (2010) 1.87
Polarizable empirical force field for the primary and secondary alcohol series based on the classical Drude model. J Chem Theory Comput (2007) 1.86
Multidomain assembled states of Hck tyrosine kinase in solution. Proc Natl Acad Sci U S A (2010) 1.79
Polarizable empirical force field for aromatic compounds based on the classical drude oscillator. J Phys Chem B (2007) 1.77
An emerging consensus on voltage-dependent gating from computational modeling and molecular dynamics simulations. J Gen Physiol (2012) 1.72
Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories. Proc Natl Acad Sci U S A (2009) 1.70
Force field bias in protein folding simulations. Biophys J (2009) 1.67
Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations. J Chem Phys (2008) 1.66
A rapid coarse residue-based computational method for x-ray solution scattering characterization of protein folds and multiple conformational states of large protein complexes. Biophys J (2009) 1.63
PBEQ-Solver for online visualization of electrostatic potential of biomolecules. Nucleic Acids Res (2008) 1.61
Structural basis of two-stage voltage-dependent activation in K+ channels. Proc Natl Acad Sci U S A (2003) 1.61
Electrostatics of ion stabilization in a ClC chloride channel homologue from Escherichia coli. J Mol Biol (2004) 1.61
Understanding the dielectric properties of liquid amides from a polarizable force field. J Phys Chem B (2008) 1.57
The N-terminal end of the catalytic domain of SRC kinase Hck is a conformational switch implicated in long-range allosteric regulation. Structure (2005) 1.53
Molecular basis of proton blockage in aquaporins. Structure (2004) 1.51
Electrostatics of the intracellular vestibule of K+ channels. J Mol Biol (2005) 1.48
Free energy landscape of A-DNA to B-DNA conversion in aqueous solution. J Am Chem Soc (2005) 1.44
Src kinase conformational activation: thermodynamics, pathways, and mechanisms. PLoS Comput Biol (2008) 1.43
Structural determinants of proton blockage in aquaporins. J Mol Biol (2004) 1.43
Simulated x-ray scattering of protein solutions using explicit-solvent models. J Chem Phys (2009) 1.43
The ionization state and the conformation of Glu-71 in the KcsA K(+) channel. Biophys J (2002) 1.41
High-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD. J Phys Chem Lett (2011) 1.41
Molecular dynamics study of hydration in ethanol-water mixtures using a polarizable force field. J Phys Chem B (2005) 1.39
Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field. J Chem Theory Comput (2010) 1.39
Atomistic view of the conformational activation of Src kinase using the string method with swarms-of-trajectories. Biophys J (2009) 1.37
Parametrization, molecular dynamics simulation, and calculation of electron spin resonance spectra of a nitroxide spin label on a polyalanine alpha-helix. J Phys Chem B (2008) 1.36
In search of a consensus model of the resting state of a voltage-sensing domain. Neuron (2011) 1.36
Grand canonical Monte Carlo simulations of water in protein environments. J Chem Phys (2004) 1.36
Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations. J Chem Theory Comput (2010) 1.35
Architecture and assembly of the Gram-positive cell wall. Mol Microbiol (2013) 1.34
Computation of Absolute Hydration and Binding Free Energy with Free Energy Perturbation Distributed Replica-Exchange Molecular Dynamics (FEP/REMD). J Chem Theory Comput (2009) 1.30
On the potential functions used in molecular dynamics simulations of ion channels. Biophys J (2002) 1.29
On the structural basis of modal gating behavior in K(+) channels. Nat Struct Mol Biol (2010) 1.29
Three-dimensional architecture of membrane-embedded MscS in the closed conformation. J Mol Biol (2007) 1.27
Multifrequency electron spin resonance spectra of a spin-labeled protein calculated from molecular dynamics simulations. J Am Chem Soc (2009) 1.25
Standard binding free energies from computer simulations: What is the best strategy? J Chem Theory Comput (2013) 1.24
Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field. J Chem Theory Comput (2010) 1.24
On the origin of the electrostatic potential difference at a liquid-vacuum interface. J Chem Phys (2008) 1.23
Intermediate state trapping of a voltage sensor. J Gen Physiol (2012) 1.20
Ion selectivity of the KcsA channel: a perspective from multi-ion free energy landscapes. J Mol Biol (2010) 1.19
Building Markov state models along pathways to determine free energies and rates of transitions. J Chem Phys (2008) 1.18
The activated state of a sodium channel voltage sensor in a membrane environment. Proc Natl Acad Sci U S A (2010) 1.18
Anatomy of a structural pathway for activation of the catalytic domain of Src kinase Hck. Proteins (2007) 1.16
Molecular dynamics simulations of the influenza hemagglutinin fusion peptide in micelles and bilayers: conformational analysis of peptide and lipids. J Mol Biol (2005) 1.16
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Rapid intracellular TEA block of the KcsA potassium channel. Biophys J (2004) 1.15
Recovery from slow inactivation in K+ channels is controlled by water molecules. Nature (2013) 1.15
Explaining why Gleevec is a specific and potent inhibitor of Abl kinase. Proc Natl Acad Sci U S A (2013) 1.14
A theoretical study of aqueous solvation of K comparing ab initio, polarizable, and fixed-charge models. J Chem Theory Comput (2007) 1.13
Mechanism of intracellular block of the KcsA K+ channel by tetrabutylammonium: insights from X-ray crystallography, electrophysiology and replica-exchange molecular dynamics simulations. J Mol Biol (2006) 1.12
Two mechanisms of ion selectivity in protein binding sites. Proc Natl Acad Sci U S A (2010) 1.12
Long-pore electrostatics in inward-rectifier potassium channels. J Gen Physiol (2008) 1.12
Gramicidin channels. IEEE Trans Nanobioscience (2005) 1.12
Modeling the structure of the StART domains of MLN64 and StAR proteins in complex with cholesterol. J Lipid Res (2006) 1.08
Flexibility and charge asymmetry in the activation loop of Src tyrosine kinases. Proteins (2009) 1.08
Simulating electron spin resonance spectra of nitroxide spin labels from molecular dynamics and stochastic trajectories. J Chem Phys (2008) 1.06
Many-body polarization effects and the membrane dipole potential. J Am Chem Soc (2009) 1.06
A structural model for K2P potassium channels based on 23 pairs of interacting sites and continuum electrostatics. J Gen Physiol (2009) 1.05
Comment on "Probing the thermodynamics of competitive ion binding using minimum energy structures". J Phys Chem B (2012) 1.05
AUTOMATED FORCE FIELD PARAMETERIZATION FOR NON-POLARIZABLE AND POLARIZABLE ATOMIC MODELS BASED ON AB INITIO TARGET DATA. J Chem Theory Comput (2013) 1.05
A conformational intermediate in glutamate receptor activation. Neuron (2013) 1.05
Structural refinement from restrained-ensemble simulations based on EPR/DEER data: application to T4 lysozyme. J Phys Chem B (2013) 1.04
The binding of antibiotics in OmpF porin. Structure (2012) 1.04
Molecular dynamics investigation of the ω-current in the Kv1.2 voltage sensor domains. Biophys J (2012) 1.03
Absolute binding free energy calculations of sparsomycin analogs to the bacterial ribosome. J Phys Chem B (2010) 1.03
Efficient determination of protein-protein standard binding free energies from first principles. J Chem Theory Comput (2013) 1.02
Critical assessment of a proposed model of Shaker. FEBS Lett (2004) 1.02
Binding specificity of SH2 domains: insight from free energy simulations. Proteins (2009) 1.02
Ion selectivity of alpha-hemolysin with beta-cyclodextrin adapter. II. Multi-ion effects studied with grand canonical Monte Carlo/Brownian dynamics simulations. J Phys Chem B (2010) 1.02
Atomic constraints between the voltage sensor and the pore domain in a voltage-gated K+ channel of known structure. J Gen Physiol (2008) 1.02
A polarizable force field of dipalmitoylphosphatidylcholine based on the classical Drude model for molecular dynamics simulations of lipids. J Phys Chem B (2013) 1.01
Structural basis of a protein partner switch that regulates the general stress response of α-proteobacteria. Proc Natl Acad Sci U S A (2012) 1.00
Determination of membrane-insertion free energies by molecular dynamics simulations. Biophys J (2012) 0.99
On the utilization of energy minimization to the study of ion selectivity. Biophys J (2009) 0.99