[HTML][HTML] Biomolecular Simulations with the Three-Dimensional Reference Interaction Site Model with the Kovalenko-Hirata Closure Molecular Solvation Theory

D Roy, A Kovalenko - International Journal of Molecular Sciences, 2021 - mdpi.com
… of proteins and peptides related to neurodegeneration, protein… solvent accessible surface
area (SASA) nonpolar solvation … -KH molecular solvation theory deals with liquid state. Thus, a …

Free Energy Density of a Fluid and Its Role in Solvation and Binding

MK Gilson, T Kurtzman - Journal of Chemical Theory and …, 2024 - ACS Publications
… ϕ P&L (R)is the solvation free energy density fields around the free protein (P) and ligand (L…
MIE derivation also may be more transparent to researchers not versed in liquid state theory, …

A molecular solvation theory simulation of liquid alkyl esters of acetic acid with the 3D Reference Interaction Site Model

D Roy, A Kovalenko - Journal of Molecular Liquids, 2021 - Elsevier
… in the existing literature, available experimental solvation free energy of … solvation theory is
used in this study for liquid state simulation… The distribution function and its first derivative are …

[HTML][HTML] Accurate determination of solvation free energies of neutral organic compounds from first principles

L Pereyaslavets, G Kamath, O Butin, A Illarionov… - Nature …, 2022 - nature.com
… The liquid state properties are important in their own right, … : eg, protein shape and behavior,
protein–ligand complexes and … The scripts, tools, and data used in this work are available

Solvation Thermodynamics and Free Energy Surfaces of Intrinsically Disordered Proteins (IDPs) in Aqueous Solutions

S Maiti - 2024 - keep.lib.asu.edu
proteins and bioinformatics analyses of newly available … of the molecule in its liquid state.
This fitting process is commonly … By correctly incorporating the bias potential, we can derive the …

… Toolbox for Computational Analysis in Rational Drug Discovery: Using Biomolecular Solvation to Predict Thermodynamic, Kinetic and Structural Properties of Protein …

T Hüfner - 2019 - archiv.ub.uni-marburg.de
… the previous subsection about the origin and need to design … are often faster than the timescale
accessible by NMR, water-… experimentally derived values of liquid state properties (such …

Solvation thermodynamics of neutral and charged solutes using the solvation‐layer interface condition continuum dielectric model

A Mehdizadeh Rahimi, A Molavi Tabrizi… - … Journal of Quantum …, 2019 - Wiley Online Library
… entropies for the Mobley test set, which are available as … , for example, drug-protein binding
and protein structure-function … Other recent studies with liquid-state theories have shown …

Simple parameter-free bridge functionals for molecular density functional theory. Application to hydrophobic solvation

D Borgis, S Luukkonen, L Belloni… - The Journal of Physical …, 2020 - ACS Publications
… stability of protein structures, in the protein folding process, … , as usual in the liquid state
theories, is known analytically as … reference simulation results are available: (1) The solvation of a …

Temperature, hydrostatic pressure, and osmolyte effects on liquid–liquid phase separation in protein condensates: physical chemistry and biological implications

H Cinar, Z Fetahaj, S Cinar, RM Vernon… - … A European Journal, 2019 - Wiley Online Library
… very scarce and not available for protein solutions to date. … in combination with a liquid-state
theoretical approach.42, 76, … be a consequence of peculiar solvation effects similar to those …

Assessment of scaled particle theory predictions of the convergence of solvation entropies

HS Ashbaugh - Fluid Phase Equilibria, 2021 - Elsevier
… hard sphere diameter while neglecting liquid state inter-molecular … Expansion of the
available protein folding thermodynamic … In summary, we have examined the origin of solvation