A review of methods for the calculation of solution free energies and the modelling of systems in solution
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 …
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 …
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 …
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
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 …
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 …
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 …
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 …
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
In this review we will discuss how computational methods, and in particular classical
molecular dynamics simulations, can be used to calculate solubility of pharmaceutically …
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
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 …
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 …
organic solutes, including 125 drugs and related heterocycles, in aqueous solution. The …