MCTBI: a web server for predicting metal ion effects in RNA structures

Monte Carlo Tightly Bound Ion Model: Predicting Ion-Binding Properties of RNA with Ion Correlations and Fluctuations

(2016) Li-Zhen Sun et al.   Journal of Chemical Theory and Computation

The solution structural ensembles of RNA kink-turn motifs and their protein complexes

(2016) Xuesong Shi et al.   Nature Chemical Biology

Ultrahigh-resolution centrosymmetric crystal structure of Z-DNA reveals the massive presence of alternate conformations

(2016) Pawel Drozdzal et al.   Acta Crystallographica Section D-Structural Biology

Statistical investigation of surface bound ions and further development of BION server to include pH and salt dependence

(2015) Marharyta Petukh et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Cation–Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting

(2015) Magdalena Gebala et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

How do metal ions direct ribozyme folding?

(2015) Natalia A. Denesyuk et al.   Nature Chemistry

Multivalent ion-mediated nucleic acid helix-helix interactions: RNA versus DNA

(2015) Yuan-Yan Wu et al.   NUCLEIC ACIDS RESEARCH

Nuclear factor 90 uses an ADAR2-like binding mode to recognize specific bases in dsRNA

(2015) Uma Jayachandran et al.   NUCLEIC ACIDS RESEARCH

Competitive interaction of monovalent cations with DNA from 3D-RISM

(2015) George M. Giambaşu et al.   NUCLEIC ACIDS RESEARCH

Generalized Manning Condensation Model Captures the RNA Ion Atmosphere

(2015) Ryan L. Hayes et al.   PHYSICAL REVIEW LETTERS

Understanding the kinetic mechanism of RNA single base pair formation

(2015) Xiaojun Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural and Dynamic Basis for Low-Affinity, High-Selectivity Binding of L-Glutamine by the Glutamine Riboswitch

(2015) Aiming Ren et al.   Cell Reports

Understanding Nucleic Acid–Ion Interactions

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

Ion Counting from Explicit-Solvent Simulations and 3D-RISM

(2014) George M. Giambaşu et al.   BIOPHYSICAL JOURNAL

Free energy of RNA-counterion interactions in a tight-binding model computed by a discrete space mapping

(2014) Paul S. Henke et al.   JOURNAL OF CHEMICAL PHYSICS

Recent progress in adapting Poisson–Boltzmann methods to molecular simulations

(2014) Li Xiao et al.   JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY

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

(2014) Jinwei Zhang et al.   STRUCTURE

Quantifying Coulombic and Solvent Polarization-Mediated Forces Between DNA Helices

(2013) Zhaojian He et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Calculations of the Electric Fields in Liquid Solutions

(2013) Stephen D. Fried et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Exploring the electrostatic energy landscape for tetraloop–receptor docking

(2013) Zhaojian He et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

(2012) Serdal Kirmizialtin et al.   BIOPHYSICAL JOURNAL

Ions and RNAs: Free Energies of Counterion-Mediated RNA Fold Stabilities

(2012) C. H. Mak et al.   Journal of Chemical Theory and Computation

Predicting Ion–Nucleic Acid Interactions by Energy Landscape-Guided Sampling

(2012) Zhaojian He et al.   Journal of Chemical Theory and Computation

Competitive Binding of Cations to Duplex DNA Revealed through Molecular Dynamics Simulations

(2012) Jejoong Yoo et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Magnesium Fluctuations Modulate RNA Dynamics in the SAM-I Riboswitch

(2012) Ryan L. Hayes et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

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

Effects of Mg2+on the Free Energy Landscape for Folding a Purine Riboswitch RNA

(2011) Desirae Leipply et al.   BIOCHEMISTRY

MetalionRNA: computational predictor of metal-binding sites in RNA structures

(2011) Anna Philips et al.   BIOINFORMATICS

Evidence for a Thermodynamically Distinct Mg2+Ion Associated with Formation of an RNA Tertiary Structure

(2011) Desirae Leipply et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Predicting Ion Binding Properties for RNA Tertiary Structures

(2010) Zhi-Jie Tan et al.   BIOPHYSICAL JOURNAL

Computational Exploration of Mobile Ion Distributions around RNA Duplex

(2010) Serdal Kirmizialtin et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular Simulation Studies of Monovalent Counterion-Mediated Interactions in a Model RNA Kissing Loop

(2009) Alan A. Chen et al.   JOURNAL OF MOLECULAR BIOLOGY

Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch

(2009) Nadia Kulshina et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structural basis of ligand binding by a c-di-GMP riboswitch

(2009) Kathryn D Smith et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

How RNA Unfolds and Refolds

(2008) Pan T.X. Li et al.   Annual Review of Biochemistry

RNA Folding: Conformational Statistics, Folding Kinetics, and Ion Electrostatics

(2008) Shi-Jie Chen   Annual Review of Biophysics

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

(2008) David E. Draper   BIOPHYSICAL JOURNAL

Salt Dependence of Nucleic Acid Hairpin Stability

(2008) Zhi-Jie Tan et al.   BIOPHYSICAL JOURNAL

Density functional study on the structural and thermodynamic properties of aqueous DNA-electrolyte solution in the framework of cell model

(2008) Ke Wang et al.   JOURNAL OF CHEMICAL PHYSICS

Critical Assessment of Nucleic Acid Electrostatics via Experimental and Computational Investigation of an Unfolded State Ensemble

(2008) Yu Bai et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structural insights into amino acid binding and gene control by a lysine riboswitch

(2008) Alexander Serganov et al.   NATURE

Continuum molecular electrostatics, salt effects, and counterion binding—A review of the Poisson–Boltzmann theory and its modifications

(2007) Paweł Grochowski et al.   BIOPOLYMERS