| scholarly article | Q13442814 |
| P50 | author | Ken A. Dill | Q6387211 |
| David L. Mobley | Q55143475 | ||
| Philippe H Hünenberger | Q58140190 | ||
| Gabriel J Rocklin | Q58870035 | ||
| P2860 | cites work | Electrostatics of nanosystems: application to microtubules and the ribosome | Q24555224 |
| Comparison of simple potential functions for simulating liquid water | Q26778447 | ||
| Artificial protein cavities as specific ligand-binding templates: characterization of an engineered heterocyclic cation-binding site that preserves the evolved specificity of the parent protein | Q27637510 | ||
| Excision of a proposed electron transfer pathway in cytochromecperoxidase and its replacement by a ligand-binding channel | Q27638883 | ||
| Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site | Q27657572 | ||
| Blind Prediction of Charged Ligand Binding Affinities in a Model Binding Site | Q27679245 | ||
| GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation | Q27860944 | ||
| Comparison of multiple Amber force fields and development of improved protein backbone parameters | Q27861040 | ||
| Die Berechnung optischer und elektrostatischer Gitterpotentiale | Q29012957 | ||
| Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties | Q30427121 | ||
| Statistically optimal analysis of samples from multiple equilibrium states | Q30438437 | ||
| On the Dielectric "Constant" of Proteins: Smooth Dielectric Function for Macromolecular Modeling and Its Implementation in DelPhi | Q30538681 | ||
| Orientational steering in enzyme-substrate association: ionic strength dependence of hydrodynamic torque effects | Q33367817 | ||
| Calculation of absolute protein-ligand binding free energy from computer simulations | Q33784404 | ||
| The statistical-thermodynamic basis for computation of binding affinities: a critical review | Q33915676 | ||
| Gaussian fluctuations and linear response in an electron transfer protein | Q34066912 | ||
| Electrostatic contributions to T4 lysozyme stability: solvent-exposed charges versus semi-buried salt bridges | Q34178635 | ||
| Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins | Q34178775 | ||
| Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy | Q34184435 | ||
| Generalized Born model with a simple, robust molecular volume correction | Q34287102 | ||
| Viewpoint 9--molecular structure of aqueous interfaces | Q34358308 | ||
| The GROMOS software for biomolecular simulation: GROMOS05. | Q34457783 | ||
| The hidden energetics of ligand binding and activation in a glutamate receptor | Q34786873 | ||
| Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials | Q35051978 | ||
| On the charge and molecule based summations of solvent electrostatic potentials and the validity of electrostatic linear response in water | Q36274597 | ||
| Modeling electrostatic effects in proteins | Q36627431 | ||
| On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review | Q36849786 | ||
| Ab initio molecular dynamics calculations of ion hydration free energies | Q37330261 | ||
| Multilevel Summation of Electrostatic Potentials Using Graphics Processing Units | Q37344800 | ||
| A proposal for the revision of molecular boundary typology | Q37774337 | ||
| Poisson-Boltzmann Calculations: van der Waals or Molecular Surface? | Q38072041 | ||
| Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study | Q38324310 | ||
| Free energy via molecular simulation: applications to chemical and biomolecular systems | Q38648060 | ||
| Calculation of Derivative Thermodynamic Hydration and Aqueous Partial Molar Properties of Ions Based on Atomistic Simulations | Q39541617 | ||
| Single mutation induced H3N2 hemagglutinin antibody neutralization: a free energy perturbation study | Q39987453 | ||
| Protein-Ligand Binding from Distancefield Distances and Hamiltonian Replica Exchange Simulations | Q40296720 | ||
| Efficient Combination of Environment Change and Alchemical Perturbation within the Enveloping Distribution Sampling (EDS) Scheme: Twin-System EDS and Application to the Determination of Octanol-Water Partition Coefficients | Q40298316 | ||
| Electrostatic contribution to the binding stability of protein-protein complexes. | Q40305520 | ||
| On the origin of the electrostatic potential difference at a liquid-vacuum interface | Q41766980 | ||
| Reducing grid-dependence in finite-difference Poisson-Boltzmann calculations | Q41908438 | ||
| Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study | Q42536182 | ||
| On the Dielectric Boundary in Poisson-Boltzmann Calculations | Q42542841 | ||
| Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation | Q43013072 | ||
| Length scales and interfacial potentials in ion hydration | Q44745281 | ||
| Surface potential of the water liquid-vapor interface | Q45061810 | ||
| Computation of methodology-independent single-ion solvation properties from molecular simulations. IV. Optimized Lennard-Jones interaction parameter sets for the alkali and halide ions in water | Q45073969 | ||
| Molecular dynamics of the water liquid-vapor interface. | Q45999630 | ||
| The vapor-liquid interface potential of (multi)polar fluids and its influence on ion solvation | Q46307241 | ||
| Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations | Q46477254 | ||
| Comment on "Study on the liquid-vapor interface of water. I. Simulation results of thermodynamic properties and orientational structure". | Q46855731 | ||
| Ball-and-Stick Local Elevation Umbrella Sampling: Molecular Simulations Involving Enhanced Sampling within Conformational or Alchemical Subspaces of Low Internal Dimensionalities, Minimal Irrelevant Volumes, and Problem-Adapted Geometries. | Q51037936 | ||
| Enhanced Conformational Sampling in Molecular Dynamics Simulations of Solvated Peptides: Fragment-Based Local Elevation Umbrella Sampling. | Q51037946 | ||
| DynamO: a free O(N) general event-driven molecular dynamics simulator. | Q51528352 | ||
| Computation of methodology-independent single-ion solvation properties from molecular simulations. III. Correction terms for the solvation free energies, enthalpies, entropies, heat capacities, volumes, compressibilities, and expansivities of solvat | Q51578620 | ||
| Electronic effects on the surface potential at the vapor-liquid interface of water. | Q51616530 | ||
| Computation of methodology-independent ionic solvation free energies from molecular simulations. II. The hydration free energy of the sodium cation. | Q51630155 | ||
| Computation of methodology-independent ionic solvation free energies from molecular simulations. I. The electrostatic potential in molecular liquids. | Q51630813 | ||
| Comment on "Ab initio molecular dynamics calculation of ion hydration free energies" [J. Chem. Phys. 130, 204507 (2009)]. | Q51673391 | ||
| Molecular dynamics simulations of a reversibly folding beta-heptapeptide in methanol: influence of the treatment of long-range electrostatic interactions. | Q51812988 | ||
| Calculation of Standard Binding Free Energies: Aromatic Molecules in the T4 Lysozyme L99A Mutant. | Q53190267 | ||
| An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware. | Q53497664 | ||
| Anton, a special-purpose machine for molecular dynamics simulation | Q56019494 | ||
| Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems | Q56750591 | ||
| Molecular dynamics simulations at constant pressure and/or temperature | Q56879286 | ||
| Do electrostatic interactions destabilize protein-nucleic acid binding? | Q57132496 | ||
| Limitations of atom-centered dielectric functions in implicit solvent models | Q57133539 | ||
| Evaluation of Poisson solvation models using a hybrid explicit/implicit solvent method | Q57133763 | ||
| Rationalization of the dielectric properties of common three-site water models in terms of their force field parameters | Q57831783 | ||
| Free energy of hydration of a molecular ionic solute: Tetramethylammonium ion | Q57875356 | ||
| Reply to Comment on “Electrostatic Potentials and Free Energies of Solvation of Polar and Charged Molecules” | Q57875388 | ||
| Electrostatic Potentials and Free Energies of Solvation of Polar and Charged Molecules | Q57875442 | ||
| Ion sizes and finite-size corrections for ionic-solvation free energies | Q57875473 | ||
| Electrostatic potential of a homogeneously charged square and cube in two and three dimensions | Q57875527 | ||
| Free Energy of Ionic Hydration | Q57875536 | ||
| Hydration free energy of water | Q57875595 | ||
| Correlations and free energies in restricted primitive model descriptions of electrolytes | Q57875652 | ||
| Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program | Q57975320 | ||
| New Interaction Parameters for Charged Amino Acid Side Chains in the GROMOS Force Field | Q58005486 | ||
| A Highly Parallelized Special-Purpose Computer for Many-Body Simulations with an Arbitrary Central Force: MD-GRAPE | Q58488772 | ||
| Poisson-Boltzmann Calculations: van der Waals or Molecular Surface? | Q58881112 | ||
| Understanding the Surface Potential of Water | Q59943927 | ||
| Incorporating the effect of ionic strength in free energy calculations using explicit ions | Q62002080 | ||
| How intermolecular charge transfer influences the air-water interface | Q85233762 | ||
| Accurate Estimates of Free Energy Changes in Charge Mutations | Q86825594 | ||
| P433 | issue | 18 | |
| P407 | language of work or name | English | Q1860 |
| P304 | page(s) | 184103 | |
| P577 | publication date | 2013-11-01 | |
| P1433 | published in | Journal of Chemical Physics | Q900472 |
| P1476 | title | Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects | |
| P478 | volume | 139 |
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| Q43056042 | Current and emerging opportunities for molecular simulations in structure-based drug design |
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| Q30395868 | Free Energy Perturbation Calculation of Relative Binding Free Energy between Broadly Neutralizing Antibodies and the gp120 Glycoprotein of HIV-1. |
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