Extended magnesium and calcium force field parameters for accurate ion–nucleic acid interactions in biomolecular simulations

Hofmeister Series for Metal-Cation–RNA Interactions: The Interplay of Binding Affinity and Exchange Kinetics

(2020) Sergio Cruz-León et al.   LANGMUIR

Kinetic pathways of water exchange in the first hydration shell of magnesium

(2020) Nadine Schwierz   JOURNAL OF CHEMICAL PHYSICS

Ion-Specific and pH-Dependent Hydration of Mica–Electrolyte Interfaces

(2019) Simone R. van Lin et al.   LANGMUIR

A force field of Li+, Na+, K+, Mg2+, Ca2+, Cl−, and SO42− in aqueous solution based on the TIP4P/2005 water model and scaled charges for the ions

(2019) I. M. Zeron et al.   JOURNAL OF CHEMICAL PHYSICS

Force fields for monovalent and divalent metal cations in TIP3P water based on thermodynamic and kinetic properties

(2018) Shavkat Mamatkulov et al.   JOURNAL OF CHEMICAL PHYSICS

Interaction of Na+, K+, Mg2+ and Ca2+ counter cations with RNA

(2018) Stefan K. Kolev et al.   Metallomics

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Nucleobase carbonyl groups are poor Mg2+ inner-sphere binders but excellent monovalent ion binders—a critical PDB survey

(2018) Filip Leonarski et al.   RNA

Developing force fields when experimental data is sparse: AMBER/GAFF-compatible parameters for inorganic and alkyl oxoanions

(2017) Sadra Kashefolgheta et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Solvent activity in electrolyte solutions from molecular simulation of the osmotic pressure

(2016) Maximilian Kohns et al.   JOURNAL OF CHEMICAL PHYSICS

Mg2+ions: do they bind to nucleobase nitrogens?

(2016) Filip Leonarski et al.   NUCLEIC ACIDS RESEARCH

Comparison of structural, thermodynamic, kinetic and mass transport properties of Mg2+ion models commonly used in biomolecular simulations

(2015) Maria T. Panteva et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Force Field for Mg2+, Mn2+, Zn2+, and Cd2+ Ions That Have Balanced Interactions with Nucleic Acids

(2015) Maria T. Panteva et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Parmbsc1: a refined force field for DNA simulations

(2015) Ivan Ivani et al.   NATURE METHODS

Polarizable molecular interactions in condensed phase and their equivalent nonpolarizable models

(2014) Igor V. Leontyev et al.   JOURNAL OF CHEMICAL PHYSICS

Force fields for divalent cations based on single-ion and ion-pair properties

(2013) Shavkat Mamatkulov et al.   JOURNAL OF CHEMICAL PHYSICS

Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent

(2013) Pengfei Li et al.   Journal of Chemical Theory and Computation

Ionic force field optimization based on single-ion and ion-pair solvation properties: Going beyond standard mixing rules

(2012) Maria Fyta et al.   JOURNAL OF CHEMICAL PHYSICS

Magnesium Ion–Water Coordination and Exchange in Biomolecular Simulations

(2012) Olof Allnér et al.   Journal of Chemical Theory and Computation

A Kirkwood-Buff Derived Force Field for Aqueous Alkali Halides

(2011) Moon Bae Gee et al.   Journal of Chemical Theory and Computation

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

(2011) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

Improved Parametrization of Li+, Na+, K+, and Mg2+ Ions for All-Atom Molecular Dynamics Simulations of Nucleic Acid Systems

(2011) Jejoong Yoo et al.   Journal of Physical Chemistry Letters

A Stability Concept for Metal Ion Coordination to Single-Stranded Nucleic Acids and Affinities of Individual Sites

(2010) Roland K. O. Sigel et al.   ACCOUNTS OF CHEMICAL RESEARCH

Ionic force field optimization based on single-ion and ion-pair solvation properties

(2010) Maria Fyta et al.   JOURNAL OF CHEMICAL PHYSICS

Cation specific binding with protein surface charges

(2009) B. Hess et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures

(2008) Xiang-Jun Lu et al.   Nature Protocols