Solv: An alternative continuum model implementation based on fixed atomic charges, scaled particle theory, and the atom–atom potential method
Y Minenkov - Journal of Chemical Theory and Computation, 2023 - ACS Publications
An alternative continuum model implementation is reported. The electrostatic contribution to
the solvation Gibbs free energy utilizes the noniterative conductor-like screening model of …
the solvation Gibbs free energy utilizes the noniterative conductor-like screening model of …
Calculation of the free energy of solvation from molecular dynamics simulations
PFB Gonçalves, H Stassen - Pure and applied chemistry, 2004 - degruyter.com
Molecular dynamics simulation has been employed in the computation of the free energy of
solvation for a large number of solute molecules with different chemical functionalities in the …
solvation for a large number of solute molecules with different chemical functionalities in the …
A blind challenge for computational solvation free energies: introduction and overview
JP Guthrie - The Journal of Physical Chemistry B, 2009 - ACS Publications
The accompanying set of papers arose from a recent blind challenge to computational
solvation energies. The challenge was based on a set of 63 drug-like molecules for which …
solvation energies. The challenge was based on a set of 63 drug-like molecules for which …
Solvation free energies calculated using the GB/SA model: Sensitivity of results on charge sets, protocols, and force fields
MR Reddy, MD Erion, A Agarwal… - Journal of …, 1998 - Wiley Online Library
The sensitivity of aqueous solvation free energies (SFEs), estimated using the GB/SA
continuum solvent model, on charge sets, protocols, and force fields, was studied. Simple …
continuum solvent model, on charge sets, protocols, and force fields, was studied. Simple …
Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database
G Duarte Ramos Matos, DY Kyu… - Journal of Chemical & …, 2017 - ACS Publications
Solvation free energies can now be calculated precisely from molecular simulations,
providing a valuable test of the energy functions underlying these simulations. Here we …
providing a valuable test of the energy functions underlying these simulations. Here we …
Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field
The accurate prediction of protein− ligand binding free energies is a primary objective in
computer-aided drug design. The solvation free energy of a small molecule provides a …
computer-aided drug design. The solvation free energy of a small molecule provides a …
Performance of SM6, SM8, and SMD on the SAMPL1 test set for the prediction of small-molecule solvation free energies
AV Marenich, CJ Cramer… - The Journal of Physical …, 2009 - ACS Publications
The SM6, SM8, and SMD quantum mechanical aqueous continuum solvation models are
applied to predict free energies of aqueous solvation for 61 molecules in the SAMPL1 test …
applied to predict free energies of aqueous solvation for 61 molecules in the SAMPL1 test …
Assessing the predictive power of relative binding free energy calculations for test cases involving displacement of binding site water molecules
Improved sampling methodologies, more accurate force fields, and access to longer
simulation time scales have led to an increased application of Relative Binding Free Energy …
simulation time scales have led to an increased application of Relative Binding Free Energy …
Efficient computation of the total solvation energy of small molecules via the R6 generalized Born model
B Aguilar, AV Onufriev - Journal of chemical theory and …, 2012 - ACS Publications
Efficient and accurate methodologies to compute solvation free energies of small molecules
are relevant for many biological and industrial research areas including rational drug …
are relevant for many biological and industrial research areas including rational drug …
Accurate Transferable Model for Water, n-Octanol, and n-Hexadecane Solvation Free Energies
AJ Bordner, CN Cavasotto… - The Journal of Physical …, 2002 - ACS Publications
We present a fast continuum method for the calculation of solvation free energies. It is based
on a continuum electrostatics model with MMFF94 atomic charges combined with a …
on a continuum electrostatics model with MMFF94 atomic charges combined with a …