Published in J Chem Theory Comput on March 01, 2010
Balanced Protein-Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association. J Chem Theory Comput (2014) 1.47
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All-atom polarizable force field for DNA based on the classical Drude oscillator model. J Comput Chem (2014) 1.16
Rapid parameterization of small molecules using the Force Field Toolkit. J Comput Chem (2013) 1.10
Recent Developments and Applications of the CHARMM force fields. Wiley Interdiscip Rev Comput Mol Sci (2011) 1.09
Development of CHARMM polarizable force field for nucleic acid bases based on the classical Drude oscillator model. J Phys Chem B (2010) 1.07
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Classical electrostatics for biomolecular simulations. Chem Rev (2013) 1.00
Balancing the interactions of ions, water, and DNA in the Drude polarizable force field. J Phys Chem B (2014) 0.94
Competition among Li(+), Na(+), K(+), and Rb(+) monovalent ions for DNA in molecular dynamics simulations using the additive CHARMM36 and Drude polarizable force fields. J Phys Chem B (2015) 0.91
Sampling of Organic Solutes in Aqueous and Heterogeneous Environments Using Oscillating Excess Chemical Potentials in Grand Canonical-like Monte Carlo-Molecular Dynamics Simulations. J Chem Theory Comput (2014) 0.88
A combined experimental and theoretical study of ion solvation in liquid N-methylacetamide. J Am Chem Soc (2010) 0.83
Nonadditive empirical force fields for short-chain linear alcohols: methanol to butanol. Hydration free energetics and Kirkwood-Buff analysis using charge equilibration models. J Phys Chem B (2010) 0.82
Solvation properties of N-acetyl-β-glucosamine: molecular dynamics study incorporating electrostatic polarization. J Comput Chem (2011) 0.82
Hydration Free Energy from Orthogonal Space Random Walk and Polarizable Force Field. J Chem Theory Comput (2014) 0.82
Polarizable simulations with second order interaction model (POSSIM) force field: developing parameters for protein side-chain analogues. J Comput Chem (2013) 0.82
Current status of protein force fields for molecular dynamics simulations. Methods Mol Biol (2015) 0.81
Prediction of hydration free energies for the SAMPL4 diverse set of compounds using molecular dynamics simulations with the OPLS-AA force field. J Comput Aided Mol Des (2014) 0.81
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POSSIM: Parameterizing Complete Second-Order Polarizable Force Field for Proteins. J Chem Theory Comput (2014) 0.81
Prediction of hydration free energies for aliphatic and aromatic chloro derivatives using molecular dynamics simulations with the OPLS-AA force field. J Comput Aided Mol Des (2011) 0.80
Charge equilibration force fields for molecular dynamics simulations of lipids, bilayers, and integral membrane protein systems. Biochim Biophys Acta (2011) 0.79
Using MD Simulations To Calculate How Solvents Modulate Solubility. J Chem Theory Comput (2016) 0.79
Free energetics of carbon nanotube association in pure and aqueous ionic solutions. J Phys Chem B (2012) 0.79
Matching of additive and polarizable force fields for multiscale condensed phase simulations. J Chem Theory Comput (2013) 0.78
Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations. J Am Chem Soc (2017) 0.77
Close encounters with DNA. J Phys Condens Matter (2014) 0.77
Balancing the Interactions of Mg(2+) in Aqueous Solution and with Nucleic Acid Moieties For a Polarizable Force Field Based on the Classical Drude Oscillator Model. J Phys Chem B (2016) 0.77
Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields. Biopolymers (2016) 0.76
Improving the Force Field Description of Tyrosine-Choline Cation-π Interactions: QM Investigation of Phenol-N(Me)4(+) Interactions. J Chem Theory Comput (2016) 0.75
Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates. J Comput Aided Mol Des (2017) 0.75
Evaluation of solvation free energies for small molecules with the AMOEBA polarizable force field. J Comput Chem (2016) 0.75
Close intramolecular sulfur-oxygen contacts: modified force field parameters for improved conformation generation. J Comput Aided Mol Des (2012) 0.75
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Molecular dynamics simulations of the complete satellite tobacco mosaic virus. Structure (2006) 2.71
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Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator. J Chem Theory Comput (2005) 2.02
Polarizable empirical force field for the primary and secondary alcohol series based on the classical Drude model. J Chem Theory Comput (2007) 1.86
Hydration thermodynamic properties of amino acid analogues: a systematic comparison of biomolecular force fields and water models. J Phys Chem B (2006) 1.84
Polarizable empirical force field for aromatic compounds based on the classical drude oscillator. J Phys Chem B (2007) 1.77
Understanding the dielectric properties of liquid amides from a polarizable force field. J Phys Chem B (2008) 1.57
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Molecular dynamics simulations of the d(CCAACGTTGG)(2) decamer in crystal environment: comparison of atomic point-charge, extra-point, and polarizable force fields. J Chem Phys (2004) 1.33
Combined ab initio/empirical approach for optimization of Lennard-Jones parameters for polar-neutral compounds. J Comput Chem (2002) 1.32
A Polarizable Force Field and Continuum Solvation Methodology for Modeling of Protein-Ligand Interactions. J Chem Theory Comput (2005) 1.28
Modifying the OPLS-AA force field to improve hydration free energies for several amino acid side chains using new atomic charges and an off-plane charge model for aromatic residues. J Comput Chem (2007) 1.24
Polarizable empirical force field for nitrogen-containing heteroaromatic compounds based on the classical Drude oscillator. J Comput Chem (2009) 1.22
Revised charge equilibration potential for liquid alkanes. J Phys Chem B (2008) 1.21
Efficient Simulation Method for Polarizable Protein Force Fields: Application to the Simulation of BPTI in Liquid Water. J Chem Theory Comput (2005) 1.11
Polarizability rescaling and atom-based Thole scaling in the CHARMM Drude polarizable force field for ethers. J Mol Model (2009) 1.04
Molecular dynamics simulations of DNA with polarizable force fields: convergence of an ideal B-DNA structure to the crystallographic structure. J Phys Chem B (2006) 1.01
Cation [M = H+, Li+, Na+, K+, Ca2+, Mg2+, NH4+, and NMe4+] interactions with the aromatic motifs of naturally occurring amino acids: a theoretical study. J Phys Chem A (2005) 0.94
Force field evaluation for biomolecular simulation: free enthalpies of solvation of polar and apolar compounds in various solvents. Chemphyschem (2006) 0.94
A generating equation for mixing rules and two new mixing rules for interatomic potential energy parameters. J Comput Chem (2004) 0.92
Simple cation-pi interaction between a phenyl ring and a protonated amine stabilizes an alpha-helix in water. J Am Chem Soc (2002) 0.91
The Structure of Liquid Benzene. J Chem Theory Comput (2006) 0.86
Conserved patterns in backbone torsional changes allow for single base flipping from duplex DNA with minimal distortion of the double helix. J Phys Chem B (2006) 0.83
Structure, electronic circular dichroism and Raman optical activity in the gas phase and in solution: a computational and experimental investigation. Phys Chem Chem Phys (2005) 0.79
Prediction of the aqueous solvation free energy of organic compounds by using autocorrelation of molecular electrostatic potential surface properties combined with response surface analysis. Bioorg Med Chem (2008) 0.77
Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles. J Chem Theory Comput (2012) 5.57
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
Additive empirical force field for hexopyranose monosaccharides. J Comput Chem (2008) 3.23
Calculation of absolute protein-ligand binding free energy from computer simulations. Proc Natl Acad Sci U S A (2005) 3.21
A small-molecule inhibitor of BCL6 kills DLBCL cells in vitro and in vivo. Cancer Cell (2010) 3.05
Gating charge displacement in voltage-gated ion channels involves limited transmembrane movement. Nature (2005) 2.98
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
CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model. J Comput Chem (2004) 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
CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses. J Chem Theory Comput (2009) 2.61
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
SCN5A mutations associate with arrhythmic dilated cardiomyopathy and commonly localize to the voltage-sensing mechanism. J Am Coll Cardiol (2011) 1.95
Molecular mechanism of H+ conduction in the single-file water chain of the gramicidin channel. Biophys J (2002) 1.94
Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium. J Chem Theory Comput (2012) 1.93
Primate-specific microRNA-637 inhibits tumorigenesis in hepatocellular carcinoma by disrupting signal transducer and activator of transcription 3 signaling. Hepatology (2011) 1.93
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
Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA. J Comput Chem (2011) 1.81
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
CHARMM Additive All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates and Inositol. J Chem Theory Comput (2009) 1.68
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
Molecular-level organization of saturated and polyunsaturated fatty acids in a phosphatidylcholine bilayer containing cholesterol. Biochemistry (2004) 1.62
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
Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability. Theory and applications. Theor Chem Acc (2009) 1.54
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
CHARMM additive all-atom force field for carbohydrate derivatives and its utility in polysaccharide and carbohydrate-protein modeling. J Chem Theory Comput (2011) 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
CHARMM additive all-atom force field for aldopentofuranoses, methyl-aldopentofuranosides, and fructofuranose. J Phys Chem B (2009) 1.40
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
Thymopoietin (lamina-associated polypeptide 2) gene mutation associated with dilated cardiomyopathy. Hum Mutat (2005) 1.37
Rational design of human DNA ligase inhibitors that target cellular DNA replication and repair. Cancer Res (2008) 1.36
In search of a consensus model of the resting state of a voltage-sensing domain. Neuron (2011) 1.36
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
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
Molecular dynamics studies of polyethylene oxide and polyethylene glycol: hydrodynamic radius and shape anisotropy. Biophys J (2008) 1.30
On the potential functions used in molecular dynamics simulations of ion channels. Biophys J (2002) 1.29
NMR imino proton exchange experiments on duplex DNA primarily monitor the opening of purine bases. J Am Chem Soc (2006) 1.29
On the structural basis of modal gating behavior in K(+) channels. Nat Struct Mol Biol (2010) 1.29
Prevalence of desmin mutations in dilated cardiomyopathy. Circulation (2007) 1.28
Development of a polarizable intermolecular potential function (PIPF) for liquid amides and alkanes. J Chem Theory Comput (2007) 1.28
Three-dimensional architecture of membrane-embedded MscS in the closed conformation. J Mol Biol (2007) 1.27
Reproducing crystal binding modes of ligand functional groups using Site-Identification by Ligand Competitive Saturation (SILCS) simulations. J Chem Inf Model (2011) 1.26
Multifrequency electron spin resonance spectra of a spin-labeled protein calculated from molecular dynamics simulations. J Am Chem Soc (2009) 1.25
Identification of novel extracellular signal-regulated kinase docking domain inhibitors. J Med Chem (2005) 1.25
Standard binding free energies from computer simulations: What is the best strategy? J Chem Theory Comput (2013) 1.24
On the origin of the electrostatic potential difference at a liquid-vacuum interface. J Chem Phys (2008) 1.23
Polarizable empirical force field for nitrogen-containing heteroaromatic compounds based on the classical Drude oscillator. J Comput Chem (2009) 1.22
On the importance of a funneled energy landscape for the assembly and regulation of multidomain Src tyrosine kinases. Proc Natl Acad Sci U S A (2007) 1.21
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
The activated state of a sodium channel voltage sensor in a membrane environment. Proc Natl Acad Sci U S A (2010) 1.18
Building Markov state models along pathways to determine free energies and rates of transitions. J Chem Phys (2008) 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