Development and test of highly accurate endpoint free energy methods. 2: Prediction of logarithm of n‐octanol–water partition coefficient (logP) for druglike molecules …
The logarithm of n‐octanol–water partition coefficient (logP) is frequently used as an
indicator of lipophilicity in drug discovery, which has substantial impacts on the absorption …
indicator of lipophilicity in drug discovery, which has substantial impacts on the absorption …
Ab initio quantum mechanics‐based free energy perturbation method for calculating relative solvation free energies
MR Reddy, UC Singh, MD Erion - Journal of computational …, 2007 - Wiley Online Library
A free energy perturbation (FEP) method was developed that uses ab initio quantum
mechanics (QM) for treating the solute molecules and molecular mechanics (MM) for treating …
mechanics (QM) for treating the solute molecules and molecular mechanics (MM) for treating …
Advances in binding free energies calculations: QM/MM-based free energy perturbation method for drug design
RS Rathore, M Sumakanth, MS Reddy… - Current …, 2013 - ingentaconnect.com
Multiple approaches have been devised and evaluated to computationally estimate binding
free energies. Results using a recently developed Quantum Mechanics (QM)/Molecular …
free energies. Results using a recently developed Quantum Mechanics (QM)/Molecular …
Prediction of solvation free energies of ionic solutes in neutral solvents
The prediction of solvation free energies is essential for a variety of applications. Solvation
free energies of neutral systems can be predicted quite accurately. The accuracy of …
free energies of neutral systems can be predicted quite accurately. The accuracy of …
Advances in implicit models of water solvent to compute conformational free energy and molecular dynamics of proteins at constant pH
YN Vorobjev - Advances in Protein Chemistry and Structural Biology, 2011 - Elsevier
Modern implicit solvent models for macromolecular simulations in water–proton bath are
considered. The fundamental quantity that implicit models approximate is the solute …
considered. The fundamental quantity that implicit models approximate is the solute …
Assessment of GAFF2 and OPLS-AA general force fields in combination with the water models TIP3P, SPCE, and OPC3 for the solvation free energy of druglike …
D Vassetti, M Pagliai, P Procacci - Journal of chemical theory and …, 2019 - ACS Publications
Molecular dynamics simulations have been performed to compute the solvation free energy
and the octanol/water partition coefficients for a challenging set of selected organic …
and the octanol/water partition coefficients for a challenging set of selected organic …
General parameterized SCF model for free energies of solvation in aqueous solution
CJ Cramer, DG Truhlar - Journal of the American Chemical …, 1991 - ACS Publications
We present a new general parameterization for aqueous solvation free energies of
molecules and ions in aqueous solution. It is obtained by extending a semianalytic treatment …
molecules and ions in aqueous solution. It is obtained by extending a semianalytic treatment …
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 …
Benchmarking the conductor-like polarizable continuum model (CPCM) for aqueous solvation free energies of neutral and ionic organic molecules
The conductor-like polarizable continuum model (CPCM) using several cavity models is
applied to compute aqueous solvation free energies for a number of organic molecules (30 …
applied to compute aqueous solvation free energies for a number of organic molecules (30 …
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 …