Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations
DL Mobley, CI Bayly, MD Cooper… - Journal of chemical …, 2009 - ACS Publications
Using molecular dynamics free energy simulations with TIP3P explicit solvent, we compute
the hydration free energies of 504 neutral small organic molecules and compare them to …
the hydration free energies of 504 neutral small organic molecules and compare them to …
Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent
In molecular simulations with fixed-charge force fields, the choice of partial atomic charges
influences numerous computed physical properties, including binding free energies. Many …
influences numerous computed physical properties, including binding free energies. Many …
Predictions of hydration free energies from all-atom molecular dynamics simulations
DL Mobley, CI Bayly, MD Cooper… - The Journal of Physical …, 2009 - ACS Publications
Here, we computed the aqueous solvation (hydration) free energies of 52 small drug-like
molecules using an all-atom force field in explicit water. This differs from previous studies in …
molecules using an all-atom force field in explicit water. This differs from previous studies in …
Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations
PV Klimovich, DL Mobley - Journal of Computer-Aided Molecular Design, 2010 - Springer
Molecular dynamics simulations in explicit solvent were applied to predict the hydration free
energies for 23 small organic molecules in blind SAMPL2 test. We found good agreement …
energies for 23 small organic molecules in blind SAMPL2 test. We found good agreement …
Computations of absolute solvation free energies of small molecules using explicit and implicit solvent model
Accurate determination of absolute solvation free energy plays a critical role in numerous
areas of biomolecular modeling and drug discovery. A quantitative representation of ligand …
areas of biomolecular modeling and drug discovery. A quantitative representation of ligand …
Hydration of amino acid side chains: Nonpolar and electrostatic contributions calculated from staged molecular dynamics free energy simulations with explicit water …
A staged protocol for performing molecular dynamics solvation free energy simulations is
described. The solvation free energy is expressed in terms of nonpolar and electrostatic …
described. The solvation free energy is expressed in terms of nonpolar and electrostatic …
Computation of methodology-independent ionic solvation free energies from molecular simulations. II. The hydration free energy of the sodium cation
MA Kastenholz, PH Hünenberger - The Journal of chemical physics, 2006 - pubs.aip.org
The raw ionic solvation free energies computed from atomistic explicit-solvent simulations
are extremely sensitive to the boundary conditions finite or periodic system, system shape …
are extremely sensitive to the boundary conditions finite or periodic system, system shape …
Hydration free energies of molecular ions from theory and simulation
We present a theoretical/computational framework for accurate calculation of hydration free
energies of ionized molecular species. The method is based on a molecular theory, 3D …
energies of ionized molecular species. The method is based on a molecular theory, 3D …
Treating entropy and conformational changes in implicit solvent simulations of small molecules
Implicit solvent models are increasingly popular for estimating aqueous solvation (hydration)
free energies in molecular simulations and other applications. In many cases, parameters for …
free energies in molecular simulations and other applications. In many cases, parameters for …
Electrostatic potentials and free energies of solvation of polar and charged molecules
Theories of solvation free energies often involve electrostatic potentials at the position of a
solute charge. Simulation calculations that apply cutoffs and periodic boundary conditions …
solute charge. Simulation calculations that apply cutoffs and periodic boundary conditions …