Unraveling Mg 2+ –RNA binding with atomistic molecular dynamics

Binding of metals to purine N7 nitrogen atoms and implications for nucleic acids: A CSD survey

(2016) Filip Leonarski et al.   INORGANICA CHIMICA ACTA

Structural, dynamical and catalytic interplay between Mg 2+ ions and RNA. Vices and virtues of atomistic simulations

(2016) Lorenzo Casalino et al.   INORGANICA CHIMICA ACTA

Studying metal ion binding properties of a three-way junction RNA by heteronuclear NMR

(2016) Simona Bartova et al.   JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY

An implicit divalent counterion force field for RNA molecular dynamics

(2016) Paul S. Henke et al.   JOURNAL OF CHEMICAL PHYSICS

Empirical Corrections to the Amber RNA Force Field with Target Metadynamics

(2016) Alejandro Gil-Ley et al.   Journal of Chemical Theory and Computation

Divalent Ion Dependent Conformational Changes in an RNA Stem-Loop Observed by Molecular Dynamics

(2016) Christina Bergonzo et al.   Journal of Chemical Theory and Computation

RNA folding pathways in stop motion

(2016) Sandro Bottaro et al.   NUCLEIC ACIDS RESEARCH

Opposing Effects of Multivalent Ions on the Flexibility of DNA and RNA

(2016) Aleksander V. Drozdetski et al.   PHYSICAL REVIEW LETTERS

Magnesium Dependence of the RNA Free Energy Landscape

(2015) Ryan L. Hayes et al.   BIOPHYSICAL JOURNAL

Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations

(2015) Francesco Di Palma et al.   BMC BIOINFORMATICS

Molecular dynamics simulations of solutions at constant chemical potential

(2015) C. Perego et al.   JOURNAL OF CHEMICAL PHYSICS

Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering

(2015) Alejandro Gil-Ley et al.   Journal of Chemical Theory and Computation

Stacking in RNA: NMR of Four Tetramers Benchmark Molecular Dynamics

(2015) David E. Condon et al.   Journal of Chemical Theory and Computation

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

Magnesium-binding architectures in RNA crystal structures: validation, binding preferences, classification and motif detection

(2015) Heping Zheng et al.   NUCLEIC ACIDS RESEARCH

The role of an active site Mg2+ in HDV ribozyme self-cleavage: insights from QM/MM calculations

(2015) Vojtěch Mlýnský et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields

(2015) Christina Bergonzo et al.   RNA

Understanding Nucleic Acid–Ion Interactions

(2014) Jan Lipfert et al.   Annual Review of Biochemistry

The rise of regulatory RNA

(2014) Kevin V. Morris et al.   NATURE REVIEWS GENETICS

Ab Initio Molecular Dynamics of Na+ and Mg2+ Countercations at the Backbone of RNA in Water Solution

(2013) Stefan Kolev et al.   ACS Chemical Biology

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide

(2013) Christina Bergonzo et al.   Journal of Chemical Theory and Computation

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

The Ionic Atmosphere around A-RNA: Poisson-Boltzmann and Molecular Dynamics Simulations

(2012) Serdal Kirmizialtin et al.   BIOPHYSICAL JOURNAL

RNA and Its Ionic Cloud: Solution Scattering Experiments and Atomically Detailed Simulations

(2012) Serdal Kirmizialtin et al.   BIOPHYSICAL JOURNAL

Cations in charge: magnesium ions in RNA folding and catalysis

(2012) Jessica C Bowman et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Magnesium Ion–Water Coordination and Exchange in Biomolecular Simulations

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

Metadynamics with Adaptive Gaussians

(2012) Davide Branduardi et al.   Journal of Chemical Theory and Computation

On the Use of Experimental Observations to Bias Simulated Ensembles

(2012) Jed W. Pitera et al.   Journal of Chemical Theory and Computation

Non-specific binding of Na + and Mg 2+ to RNA determined by force spectroscopy methods

(2012) C. V. Bizarro et al.   NUCLEIC ACIDS RESEARCH

Entropic origin of Mg2+-facilitated RNA folding

(2012) J. L. Fiore et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Capturing the essence of folding and functions of biomolecules using coarse-grained models

(2011) Changbong Hyeon et al.   Nature Communications

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

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

Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field

(2010) Haibo Yu et al.   Journal of Chemical Theory and Computation

Bidentate RNA-magnesium clamps: On the origin of the special role of magnesium in RNA folding

(2010) A. S. Petrov et al.   RNA

Frequency and Effect of the Binding of Mg2+, Mn2+, and Co2+Ions on the Guanine Base in Watson−Crick and Reverse Watson−Crick Base Pairs

(2009) Romina Oliva et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Understanding the Adaptive Growth Strategy of Lactobacillus plantarum by In Silico Optimisation

(2009) Bas Teusink et al.   PLoS Computational Biology

RNA Folding: Thermodynamic and Molecular Descriptions of the Roles of Ions

(2008) David E. Draper   BIOPHYSICAL JOURNAL

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

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS