Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties

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

Theory and simulations for RNA folding in mixtures of monovalent and divalent cations

(2019) Hung T. Nguyen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

GROmaρs: A GROMACS-Based Toolset to Analyze Density Maps Derived from Molecular Dynamics Simulations

(2018) Rodolfo Briones et al.   BIOPHYSICAL JOURNAL

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

(2018) Filip Leonarski et al.   RNA

Hydration and Ion Pairing in Aqueous Mg2+ and Zn2+ Solutions: Force-Field Description Aided by Neutron Scattering Experiments and Ab Initio Molecular Dynamics Simulations

(2017) Elise Duboué-Dijon et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

Unraveling Mg 2+ –RNA binding with atomistic molecular dynamics

(2017) Richard A. Cunha et al.   RNA

CheckMyMetal: a macromolecular metal-binding validation tool

(2017) Heping Zheng et al.   Acta Crystallographica Section D-Structural Biology

Direct Observation of Nanosecond Water Exchange Dynamics at a Protein Metal Site

(2016) Monika Stachura et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

Accurate Description of Calcium Solvation in Concentrated Aqueous Solutions

(2014) Miriam Kohagen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Dramatic Improvement of Crystals of Large RNAs by Cation Replacement and Dehydration

(2014) Jinwei Zhang et al.   STRUCTURE

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

Taking into Account the Ion-Induced Dipole Interaction in the Nonbonded Model of Ions

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

Recovery from slow inactivation in K+ channels is controlled by water molecules

(2013) Jared Ostmeyer et al.   NATURE

Role of Ligand Binding in Structural Organization ofAddA-riboswitch Aptamer: A Molecular Dynamics Simulation

(2012) Zhou Gong et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

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

Metal-ion rescue revisited: Biochemical detection of site-bound metal ions important for RNA folding

(2012) J. K. Frederiksen et al.   RNA

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

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

(2011) Naveen Michaud-Agrawal et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Accounting for electronic polarization in non-polarizable force fields

(2011) Igor Leontyev et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins

(2010) Pavel Banáš et al.   Journal of Chemical Theory and Computation

Rational design of ion force fields based on thermodynamic solvation properties

(2009) Dominik Horinek et al.   JOURNAL OF CHEMICAL PHYSICS

Solvation Dynamics of Model Peptides Probed by Terahertz Spectroscopy. Observation of the Onset of Collective Network Motions

(2009) Benjamin Born et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

(2008) In Suk Joung et al.   JOURNAL OF PHYSICAL CHEMISTRY B

NMR and MD studies of the temperature-dependent dynamics of RNA YNMG-tetraloops

(2008) Jan Ferner et al.   NUCLEIC ACIDS RESEARCH

P-LINCS:  A Parallel Linear Constraint Solver for Molecular Simulation

(2007) Berk Hess   Journal of Chemical Theory and Computation