Solvation models: theory and validation
EO Purisima, T Sulea - Current Pharmaceutical Design, 2014 - ingentaconnect.com
Water plays an active role in many fundamental phenomena in cellular systems such as
molecular recognition, folding and conformational equilibria, reaction kinetics and phase …
molecular recognition, folding and conformational equilibria, reaction kinetics and phase …
[HTML][HTML] 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 …
Rapid prediction of solvation free energy. 2. The first-shell hydration (FiSH) continuum model
Local ordering of water in the first hydration shell around a solute is different from isotropic
bulk water. This leads to effects that are captured by explicit solvation models and missed by …
bulk water. This leads to effects that are captured by explicit solvation models and missed by …
Accurate predictions of nonpolar solvation free energies require explicit consideration of binding-site hydration
S Genheden, P Mikulskis, LH Hu… - Journal of the …, 2011 - ACS Publications
Continuum solvation methods are frequently used to increase the efficiency of computational
methods to estimate free energies. In this paper, we have evaluated how well such methods …
methods to estimate free energies. In this paper, we have evaluated how well such methods …
GridSolvate: A web server for the prediction of biomolecular hydration properties
P Setny - Journal of Chemical Information and Modeling, 2020 - ACS Publications
We present a novel web server, named gridSolvate, dedicated to the prediction of
biomolecular hydration properties. Given a solute in atomic representation, such as a protein …
biomolecular hydration properties. Given a solute in atomic representation, such as a protein …
Molecular modeling of hydration in drug design.
RL Mancera - Current Opinion in Drug Discovery & Development, 2007 - europepmc.org
The accurate prediction of the binding mode and affinity of a drug molecule to its putative
receptor is crucial for successful drug design and optimization. Modeling the role of the …
receptor is crucial for successful drug design and optimization. Modeling the role of the …
[图书][B] Solvation free energies from a coupled reference interaction site model/simulation approach
H Freedman - 2005 - search.proquest.com
Accounting for solvation in thermodynamic studies is one issue requiring further work so that
computational models may be more advantageously applied to studies of systems in …
computational models may be more advantageously applied to studies of systems in …
Fast estimation of solvation free energies for diverse chemical species
RD Boyer, RL Bryan - The Journal of Physical Chemistry B, 2012 - ACS Publications
The free energy of solvation can play an important or even dominant role in the accurate
prediction of binding affinities and various other molecular-scale interaction phenomena …
prediction of binding affinities and various other molecular-scale interaction phenomena …
A protein solvation model based on residue burial
The influence of solvent on the individual amino acids of a protein depends not simply on
their surface exposure but rather on the degree of their burial within the structure. This …
their surface exposure but rather on the degree of their burial within the structure. This …
On the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute− solvent interaction energy
RM Levy, LY Zhang, E Gallicchio… - Journal of the American …, 2003 - ACS Publications
Implicit solvent hydration free energy models are an important component of most modern
computational methods aimed at protein structure prediction, binding affinity prediction, and …
computational methods aimed at protein structure prediction, binding affinity prediction, and …