A review of methods for the calculation of solution free energies and the modelling of systems in solution

RE Skyner, JL McDonagh, CR Groom… - Physical Chemistry …, 2015 - pubs.rsc.org
Over the past decade, pharmaceutical companies have seen a decline in the number of
drug candidates successfully passing through clinical trials, though billions are still spent on …

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 …

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 …

Computations of absolute solvation free energies of small molecules using explicit and implicit solvent model

D Shivakumar, Y Deng, B Roux - Journal of Chemical Theory and …, 2009 - ACS Publications
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 …

Optimizing solute–water van der Waals interactions to reproduce solvation free energies

PS Nerenberg, B Jo, C So, A Tripathy… - The Journal of …, 2012 - ACS Publications
An accurate representation of solute–water interactions is necessary for molecular dynamics
simulations of biomolecules that reside in aqueous environments. Modern force fields and …

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 …

[HTML][HTML] Computational prediction of drug solubility in water-based systems: Qualitative and quantitative approaches used in the current drug discovery and …

CAS Bergström, P Larsson - International journal of pharmaceutics, 2018 - Elsevier
In this review we will discuss recent advances in computational prediction of solubility in
water-based solvents. Our focus is set on recent advances in predictions of biorelevant …

[HTML][HTML] Molecular simulation as a computational pharmaceutics tool to predict drug solubility, solubilization processes and partitioning

S Hossain, A Kabedev, A Parrow… - European Journal of …, 2019 - Elsevier
In this review we will discuss how computational methods, and in particular classical
molecular dynamics simulations, can be used to calculate solubility of pharmaceutically …

Calculations of solvation free energy through energy reweighting from molecular mechanics to quantum mechanics

X Jia, M Wang, Y Shao, G Konig… - Journal of chemical …, 2016 - ACS Publications
In this work, the solvation free energies of 20 organic molecules from the 4th Statistical
Assessment of the Modeling of Proteins and Ligands (SAMPL4) have been calculated. The …

Prediction of properties from simulations: free energies of solvation in hexadecane, octanol, and water

EM Duffy, WL Jorgensen - Journal of the American Chemical …, 2000 - ACS Publications
Monte Carlo (MC) statistical mechanics simulations have been carried out for more than 200
organic solutes, including 125 drugs and related heterocycles, in aqueous solution. The …