Supplemental Data RNA Kink-Turns as Molecular Elbows: Hydration, Cation Binding, and Large-Scale Dynamics (original) (raw)

Concentration-dependent and configuration-dependent interactions of monovalent ions with an RNA tetraloop

Jacob Miner

The Journal of chemical physics, 2018

View PDFchevron_right

Computational Exploration of Mobile Ion Distributions around RNA Duplex

Serdal Kirmizialtin

The Journal of Physical Chemistry B, 2010

View PDFchevron_right

Water and ion binding around RNA and DNA (C,G) oligomers

Eric Westhof

Journal of Molecular Biology, 2000

View PDFchevron_right

Ionic Mixtures and Distributions Around RNA: Atomically Detailed Simulations with Replica Exchange

Serdal Kirmizialtin

Biophysical Journal, 2009

View PDFchevron_right

RNA hydration: three nanoseconds of multiple molecular dynamics simulations of the solvated tRNAAsp anticodon hairpin

Eric Westhof

Journal of Molecular Biology, 1997

View PDFchevron_right

Large-Scale Analysis of 48 DNA and 48 RNA Tetranucleotides Studied by 1 μs Explicit-Solvent Molecular Dynamics Simulations

Michael Schrodt

Journal of Chemical Theory and Computation, 2015

View PDFchevron_right

RNA Kink-Turns as Molecular Elbows: Hydration, Cation Binding, and Large-Scale Dynamics

Filip Razga

Structure, 2006

View PDFchevron_right

Symmetric K+ and Mg2+ Ion-binding Sites in the 5S rRNA Loop E Inferred from Molecular Dynamics Simulations

Eric Westhof

Journal of Molecular Biology, 2004

View PDFchevron_right

Modelling ion binding to AA platform motifs in RNA: a continuum solvent study including conformational adaptation

Martin Zacharias

Nucleic acids research, 2001

View PDFchevron_right

Non-Watson-Crick Basepairing and Hydration in RNA Motifs: Molecular Dynamics of 5S rRNA Loop E

Neocles Leontis

Biophysical Journal, 2003

View PDFchevron_right

Differences in ion-RNA binding modes due to charge density variations explain the stability of RNA in monovalent salts

Serdal Kirmizialtin

Science Advances, 2022

View PDFchevron_right

Water and ion binding around r(UpA)12and d(TpA)12Oligomers - comparison with RNA and DNA (CpG)12 duplexes

Eric Westhof

Journal of Molecular Biology, 2001

View PDFchevron_right

Explicit ions/implicit water generalized Born model for nucleic acids

Igor Tolokh

Journal of Chemical Physics, 2018

View PDFchevron_right

A simple low-cost simulation protocol for approximate localization of structural water molecules in DNA oligonucleotides

Marçal Oliveira

Journal of the Brazilian Chemical Society, 2005

View PDFchevron_right

A short guide for molecular dynamics simulations of RNA systems

Yaser Hashem

Methods, 2009

View PDFchevron_right

Molecular Dynamics Simulations of the Anticodon Hairpin of tRNA Asp : Structuring Effects of C−H···O Hydrogen Bonds and of Long-Range Hydration Forces

Eric Westhof

Journal of the American Chemical Society, 1996

View PDFchevron_right

Refinement of Generalized Born Implicit Solvation Parameters for Nucleic Acids and Their Complexes with Proteins

Giúp ViệcPhương Nam - Dịch Vụ Giúp Việc Gia Đình

Journal of Chemical Theory and Computation, 2015

View PDFchevron_right

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

Kathleen Hall

Journal of chemical theory and computation, 2016

View PDFchevron_right

Computational investigation of the role of hydration in nucleic acid structure and function

Valery Poltev

International Journal of Quantum Chemistry, 1992

View PDFchevron_right

Simulations of the molecular dynamics of nucleic acids

Eric Westhof

Current Opinion in Structural Biology, 1998

View PDFchevron_right

Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations

Mihaly Mezei

Journal of Biosciences, 2012

View PDFchevron_right

Positively and Negatively Hydrated Counterions in Molecular Dynamics Simulations of DNA Double Helix

Sergiy Perepelytsya

Ukrainian Journal of Physics, 2020

View PDFchevron_right

Structural Insights into the Effect of Hydration and Ions on A-Tract DNA: A Molecular Dynamics Study

madhumalar arumugam

Biophysical Journal, 2003

View PDFchevron_right

Simulations of the dynamics at an RNA-protein interface

Eric Westhof

Nature Structural & Molecular Biology, 1999

View PDFchevron_right

Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules

Qingyi Yang

Journal of Computational Chemistry, 2008

View PDFchevron_right

Melting of the solvent structure around a RNA duplex: a molecular dynamics simulation study

Eric Westhof

Biophysical Chemistry, 2002

View PDFchevron_right

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

Marcia Fenley, Serdal Kirmizialtin

Biophysical Journal, 2012

View PDFchevron_right