The ion-dipole correction of the 3DRISM solvation model to accurately compute water distributions around negatively charged biomolecules
The 3D reference interaction site model (3DRISM) provides an efficient grid-based solvation
model to compute the structural and thermodynamic properties of biomolecules in aqueous …
model to compute the structural and thermodynamic properties of biomolecules in aqueous …
Solvation and hydration of proteins and nucleic acids: a theoretical view of simulation and experiment
Many theoretical, computational, and experimental techniques recently have been
successfully used for description of the solvent distribution around macromolecules. In this …
successfully used for description of the solvent distribution around macromolecules. In this …
A coarse-grain three-site-per-nucleotide model for DNA with explicit ions
The “three sites per nucleotide”(3SPN) model provides a coarse-grained representation of
nucleic acids for simulation of molecular processes. Previously, this model has relied on an …
nucleic acids for simulation of molecular processes. Previously, this model has relied on an …
Grand canonical Monte Carlo molecular and thermodynamic predictions of ion effects on binding of an oligocation (L8+) to the center of DNA oligomers
MC Olmsted, JP Bond, CF Anderson, MT Record - Biophysical journal, 1995 - cell.com
Grand canonical Monte Carlo (GCMC) simulations are reported for aqueous solutions
containing excess univalent salt (activities a+/-= 1.76–12.3 mM) and one of the following …
containing excess univalent salt (activities a+/-= 1.76–12.3 mM) and one of the following …
Surfaces affect ion pairing
In water, positive ions attract negative ions. That attraction can be modulated if a
hydrophobic surface is present near the two ions in water. Using computer simulations with …
hydrophobic surface is present near the two ions in water. Using computer simulations with …
Optimized magnesium force field parameters for biomolecular simulations with accurate solvation, ion-binding, and water-exchange properties
Magnesium ions play an essential role in many vital processes. To correctly describe their
interactions in molecular dynamics simulations, an accurate parametrization is crucial …
interactions in molecular dynamics simulations, an accurate parametrization is crucial …
Binding enthalpy calculations for a neutral host–guest pair yield widely divergent salt effects across water models
Dissolved salts are a part of the physiological milieu and can significantly influence the
kinetics and thermodynamics of various biomolecular processes, such as binding and …
kinetics and thermodynamics of various biomolecular processes, such as binding and …
Revisiting the association of cationic groove-binding drugs to DNA using a Poisson-Boltzmann approach
Proper modeling of nonspecific salt-mediated electrostatic interactions is essential to
understanding the binding of charged ligands to nucleic acids. Because the linear Poisson …
understanding the binding of charged ligands to nucleic acids. Because the linear Poisson …
Determining the locations of ions and water around DNA from X-ray scattering measurements
Nucleic acids carry a negative charge, attracting salt ions and water. Interactions with these
components of the solvent drive DNA to condense, RNA to fold, and proteins to bind. To …
components of the solvent drive DNA to condense, RNA to fold, and proteins to bind. To …
DNA and its counterions: a molecular dynamics study
P Várnai, K Zakrzewska - Nucleic acids research, 2004 - academic.oup.com
The behaviour of mobile counterions, Na+ and K+, was analysed around a B-DNA double
helix with the sequence CCATGCGCTGAC in aqueous solution during two 50 ns long …
helix with the sequence CCATGCGCTGAC in aqueous solution during two 50 ns long …