☆ 4.7 Article

Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties in SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, and TIP4P-D

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2022)

相关参考文献

注意：仅列出部分参考文献，下载原文获取全部文献信息。

Article Chemistry, Physical

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

Sergio Cruz-Leon et al.

Summary: This study optimizes the description of ion interactions with nucleic acids in simulations by adjusting combination rules, significantly improving agreement with experiments and offering a more accurate method for describing metal cations in biomolecular simulations.

JOURNAL OF CHEMICAL PHYSICS (2021)

添加到收藏夹

Article Chemistry, Physical

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

Kara K. Grotz et al.

Summary: Improvements in accurately simulating the properties of magnesium ions have been made by optimizing parameters in a larger parameter space, resulting in the reproduction of experimental properties such as solvation free energy, hydration shell oxygens distance, water exchange rate, and ion-binding sites.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)

添加到收藏夹

Article Chemistry, Physical

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

Sebastian Falkner et al.

Summary: This study investigates the water exchange mechanism between the hydration shells of Mg2+ through molecular dynamics simulations and transition path sampling. It reveals that the choice of water model and Mg2+ model influences the exchange kinetics, with different mechanisms observed depending on the force field used. The results provide insights into the impact of force field choice on exchange dynamics in biomolecular simulations.

JOURNAL OF CHEMICAL PHYSICS (2021)

添加到收藏夹

Article Chemistry, Physical

Transferable Ion Force Fields in Water from a Simultaneous Optimization of Ion Solvation and Ion-Ion Interaction

Philip Loche et al.

Summary: The study developed transferable force fields for ions using a global optimization procedure, showing high accuracy in reproducing experimental data through optimization.

JOURNAL OF PHYSICAL CHEMISTRY B (2021)

添加到收藏夹

Article Chemistry, Physical

On the transferability of ion parameters to the TIP4P/2005 water model using molecular dynamics simulations

Max F. Dopke et al.

JOURNAL OF CHEMICAL PHYSICS (2020)

添加到收藏夹

Article Chemistry, Physical

Hierarchical Ensembles of Intrinsically Disordered Proteins at Atomic Resolution in Molecular Dynamics Simulations

Lisa M. Pietrek et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)

添加到收藏夹

Article Chemistry, Multidisciplinary

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

Sergio Cruz-Leon et al.

LANGMUIR (2020)

添加到收藏夹

Article Chemistry, Physical

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

Nadine Schwierz

JOURNAL OF CHEMICAL PHYSICS (2020)

添加到收藏夹

Article Chemistry, Physical

Systematic Parametrization of Divalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models

Zhen Li et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)

添加到收藏夹

Article Multidisciplinary Sciences

Dynamic cluster formation determines viscosity and diffusion in dense protein solutions

Soeron von Buelow et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

添加到收藏夹

Article Multidisciplinary Sciences

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

Hung T. Nguyen et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

添加到收藏夹

Article Chemistry, Physical

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

I. M. Zeron et al.

JOURNAL OF CHEMICAL PHYSICS (2019)

添加到收藏夹

Article Chemistry, Physical

Why Cellular Di/Triphosphates Preferably Bind Mg2+ and Not Ca2+

Cedric Grauffel et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)

添加到收藏夹

Article Chemistry, Physical

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

Elise Duboue-Dijon et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2018)

添加到收藏夹

Article Chemistry, Physical

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

Shavkat Mamatkulov et al.

JOURNAL OF CHEMICAL PHYSICS (2018)

添加到收藏夹

Review Biochemistry & Molecular Biology

DNA aggregation induced by Mg2+ ions under different conditions

Van-Chien Bui et al.

JOURNAL OF MOLECULAR RECOGNITION (2018)

添加到收藏夹

Article Chemistry, Multidisciplinary

Water-Activated VOPO4 for Magnesium Ion Batteries

Xiao Ji et al.

NANO LETTERS (2018)

添加到收藏夹

Article Chemistry, Physical

Dispersion Correction Alleviates Dye Stacking of Single-Stranded DNA and RNA in Simulations of Single-Molecule Fluorescence Experiments

Kara K. Grotz et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2018)

添加到收藏夹

Article Biochemistry & Molecular Biology

Mg2+ ions: do they bind to nucleobase nitrogens?

Filip Leonarski et al.

NUCLEIC ACIDS RESEARCH (2017)

添加到收藏夹

Review Cell Biology

Advances in RNA molecular dynamics: a simulator's guide to RNA force fields

Sweta Vangaveti et al.

WILEY INTERDISCIPLINARY REVIEWS-RNA (2017)

添加到收藏夹

Article Multidisciplinary Sciences

Biotechnological mass production of DNA origami

Florian Praetorius et al.

NATURE (2017)

添加到收藏夹

Article Chemistry, Physical

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

Sadra Kashefolgheta et al.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2017)

添加到收藏夹

Review Chemistry, Multidisciplinary

Metal Ion Modeling Using Classical Mechanics

Pengfei Li et al.

CHEMICAL REVIEWS (2017)

添加到收藏夹

Article Chemistry, Physical

Balancing the Interactions of Mg2+ in Aqueous Solution and with Nucleic Acid Moieties For a Polarizable Force Field Based on the Classical Drude Oscillator Model

Justin A. Lemkul et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2016)

添加到收藏夹

Article Chemistry, Physical

Improved Force Field Parameters Lead to a Better Description of RNA Structure

Christina Bergonzo et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

添加到收藏夹

Article Chemistry, Multidisciplinary

Comparison of Structural, Thermodynamic, Kinetic and Mass Transport Properties of Mg2+ Ion Models Commonly used in Biomolecular Simulations

Maria T. Panteva et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2015)

添加到收藏夹

Article Chemistry, Physical

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

Maria T. Panteva et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2015)

添加到收藏夹

Article Chemistry, Physical

Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States

Stefano Piana et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2015)

添加到收藏夹

Review Physiology

MAGNESIUM IN MAN: IMPLICATIONS FOR HEALTH AND DISEASE

Jeroen H. F. de Baaij et al.

PHYSIOLOGICAL REVIEWS (2015)

添加到收藏夹

Article Chemistry, Multidisciplinary

Addressing the Instability of DNA Nanostructures in Tissue Culture

Jaeseung Hahn et al.

ACS NANO (2014)

添加到收藏夹

Article Computer Science, Interdisciplinary Applications

PLUMED 2: New feathers for an old bird

Gareth A. Tribello et al.

COMPUTER PHYSICS COMMUNICATIONS (2014)

添加到收藏夹

Article Chemistry, Physical

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

Pengfei Li et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)

添加到收藏夹

Article Chemistry, Physical

Building Force Fields: An Automatic, Systematic, and Reproducible Approach

Lee-Ping Wang et al.

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2014)

添加到收藏夹

Article Chemistry, Physical

The influence of water interfacial potentials on ion hydration in bulk water and near interfaces

Thomas L. Beck

CHEMICAL PHYSICS LETTERS (2013)

添加到收藏夹

Article Chemistry, Physical

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

Shavkat Mamatkulov et al.

JOURNAL OF CHEMICAL PHYSICS (2013)

添加到收藏夹

Article Chemistry, Physical

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

Pengfei Li et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

添加到收藏夹

Article Chemistry, Multidisciplinary

Highly Reversible Open Framework Nanoscale Electrodes for Divalent Ion Batteries

Richard Y. Wang et al.

NANO LETTERS (2013)

添加到收藏夹

Article Chemistry, Physical

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

Maria Fyta et al.

JOURNAL OF CHEMICAL PHYSICS (2012)

添加到收藏夹

Article Chemistry, Physical

Magnesium Ion-Water Coordination and Exchange in Biomolecular Simulations

Olof Allner et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)

添加到收藏夹

Article Chemistry, Physical

Simulations of A-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration

Ivana Besseova et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2012)

添加到收藏夹

Article Chemistry, Physical

A Kirkwood-Buff Derived Force Field for Aqueous Alkali Halides

Moon Bae Gee et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)

添加到收藏夹

Article Chemistry, Physical

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

Marie Zgarbova et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)

添加到收藏夹

Article Chemistry, Multidisciplinary

Software News and Updates MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations

Naveen Michaud-Agrawal et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2011)

添加到收藏夹

Article Chemistry, Physical

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

Carlos Vega et al.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2011)

添加到收藏夹

Review Chemistry, Multidisciplinary

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

Roland K. O. Sigel et al.

ACCOUNTS OF CHEMICAL RESEARCH (2010)

添加到收藏夹

Article Chemistry, Physical

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

Maria Fyta et al.

JOURNAL OF CHEMICAL PHYSICS (2010)

添加到收藏夹

Article Chemistry, Physical

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

Pavel Banas et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)

添加到收藏夹

Article Chemistry, Physical

Rational design of ion force fields based on thermodynamic solvation properties

Dominik Horinek et al.

JOURNAL OF CHEMICAL PHYSICS (2009)

添加到收藏夹

Article Multidisciplinary Sciences

Cation specific binding with protein surface charges

Berk Hess et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

添加到收藏夹

Article Chemistry, Physical

P-LINCS: A parallel linear constraint solver for molecular simulation

Berk Hess

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2008)

添加到收藏夹

Review Chemistry, Physical

Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations

In Suk Joung et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2008)

添加到收藏夹

Article Chemistry, Physical

Hydration free energies of monovalent ions in transferable intermolecular potential four point fluctuating charge water: An assessment of simulation methodology and force field performance and transferability

G. Lee Warren et al.

JOURNAL OF CHEMICAL PHYSICS (2007)

添加到收藏夹

Article Chemistry, Inorganic & Nuclear

From nucleotides to ribozymes - A comparison of their metal ion binding properties

Eva Freisinger et al.

COORDINATION CHEMISTRY REVIEWS (2007)

添加到收藏夹

Article Biophysics

Refinenement of the AMBER force field for nucleic acids:: Improving the description of α/γ conformers

Alberto Perez et al.

BIOPHYSICAL JOURNAL (2007)

添加到收藏夹

Article Chemistry, Multidisciplinary

CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes

Evelyn Mayaan et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2007)

添加到收藏夹

Review Chemistry, Multidisciplinary

Alternative roles for metal ions in enzyme catalysis and the implications for ribozyme chemistry

Roland K. O. Sigel et al.

CHEMICAL REVIEWS (2007)

添加到收藏夹

Article Chemistry, Physical

Empirical force fields for biologically active divalent metal cations in water

CS Babu et al.

JOURNAL OF PHYSICAL CHEMISTRY A (2006)

添加到收藏夹

Letter Chemistry, Physical

Solubility of simple, nonpolar compounds in TIP4P-Ew

PE Krouskop et al.

JOURNAL OF CHEMICAL PHYSICS (2006)

添加到收藏夹

Article Chemistry, Physical

A general purpose model for the condensed phases of water: TIP4P/2005

JLF Abascal et al.

JOURNAL OF CHEMICAL PHYSICS (2005)

添加到收藏夹

Article Chemistry, Physical

Computational study of dimethyl phosphate anion and its complexes with water, magnesium, and calcium

AS Petrov et al.

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY (2005)

添加到收藏夹

Article Biochemistry & Molecular Biology

The contribution of metal ions to the structural stability of the large ribosomal subunit

DJ Klein et al.

RNA (2004)

添加到收藏夹

Article Chemistry, Multidisciplinary

Development and testing of a general amber force field

JM Wang et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)

添加到收藏夹

Article Chemistry, Physical

Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew

HW Horn et al.

JOURNAL OF CHEMICAL PHYSICS (2004)

添加到收藏夹

Article Chemistry, Physical

Calculations of magnesium-nucleic acid site binding in solution

AS Petrov et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2004)

添加到收藏夹

Article Chemistry, Physical

A Kirkwood-Buff derived force field for sodium chloride in water

S Weerasinghe et al.

JOURNAL OF CHEMICAL PHYSICS (2003)

添加到收藏夹

Review Biochemistry & Molecular Biology

Metal ions in the structure and function of RNA

AM Pyle

JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY (2002)

添加到收藏夹

Article Biochemistry & Molecular Biology

Structural and catalytic chemistry of magnesium-dependent enzymes

JA Cowan

BIOMETALS (2002)

添加到收藏夹

Article Chemistry, Multidisciplinary

Magnesium ion catalyzed ATP hydrolysis

NH Williams

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2000)

添加到收藏夹

© Peeref 2019-2024. All rights reserved.