Artificial Intelligence Resolves Kinetic Pathways of Magnesium Binding to RNA

“In Silico” Seawater

(2021) Ivan M. Zeron et al.   Journal of Chemical Theory and Computation

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

(2021) Sergio Cruz-León et al.   JOURNAL OF CHEMICAL PHYSICS

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

(2021) Kara K. Grotz et al.   Journal of Chemical Theory and Computation

Kinetic pathways of water exchange in the first hydration shell of magnesium: Influence of water model and ionic force field

(2021) Sebastian Falkner et al.   JOURNAL OF CHEMICAL PHYSICS

Charge Density of Cation Determines Inner versus Outer Shell Coordination to Phosphate in RNA

(2020) Hung T. Nguyen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

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

Memory-induced acceleration and slowdown of barrier crossing

(2018) Julian Kappler 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

Time-lagged autoencoders: Deep learning of slow collective variables for molecular kinetics

(2018) Christoph Wehmeyer et al.   JOURNAL OF CHEMICAL PHYSICS

Machine Learning of Biomolecular Reaction Coordinates

(2018) Simon Brandt et al.   Journal of Physical Chemistry Letters

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

(2018) Filip Leonarski et al.   RNA

Transition path sampling of rare events by shooting from the top

(2017) Hendrik Jung et al.   JOURNAL OF CHEMICAL PHYSICS

Ultrasensitivity of Water Exchange Kinetics to the Size of Metal Ion

(2017) Yuno Lee et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Unraveling Mg 2+ –RNA binding with atomistic molecular dynamics

(2017) Richard A. Cunha et al.   RNA

Mg2+ions: do they bind to nucleobase nitrogens?

(2016) Filip Leonarski et al.   NUCLEIC ACIDS RESEARCH

Modeling Electronic Polarizability Changes in the Course of a Magnesium Ion Water Ligand Exchange Process

(2015) Igor V. Kurnikov et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Cation-induced kinetic heterogeneity of the intron–exon recognition in single group II introns

(2015) Danny Kowerko et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Understanding Nucleic Acid–Ion Interactions

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

PLUMED 2: New feathers for an old bird

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

Toward the Mechanism of Ionic Dissociation in Water

(2012) Andrew J. Ballard et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

Simulating water with rigid non-polarizable models: a general perspective

(2011) Carlos Vega 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

Controlling ribozyme activity by metal ions

(2010) Joachim Schnabl et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Polarizable Molecular Dynamics Simulation of Zn(II) in Water Using the AMOEBA Force Field

(2010) Johnny C. Wu et al.   Journal of Chemical Theory and Computation

Current Status of the AMOEBA Polarizable Force Field

(2010) Jay W. Ponder et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Multinuclear NMR studies of the interaction of metal ions with adenine-nucleotides

(2008) Zoltán Szabó   COORDINATION CHEMISTRY REVIEWS

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation