Lone Pair…π Contacts and Structure Signatures of r(UNCG) Tetraloops, Z-Turns, and Z-Steps: A WebFR3D Survey

RNA-Specific Force Field Optimization with CMAP and Reweighting

(2022) Jun Chen et al.   Journal of Chemical Information and Modeling

Contact networks in RNA: a structural bioinformatics study with a new tool

(2022) Parthajit Roy et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Toward Convergence in Folding Simulations of RNA Tetraloops: Comparison of Enhanced Sampling Techniques and Effects of Force Field Modifications

(2022) Vojtěch Mlýnský et al.   Journal of Chemical Theory and Computation

Novel eGZ-motif formed by regularly extruded guanine bases in a left-handed Z-DNA helix as a major motif behind CGG trinucleotide repeats

(2022) Ashkan Fakharzadeh et al.   NUCLEIC ACIDS RESEARCH

Developing Community Resources for Nucleic Acid Structures

(2022) Helen M. Berman et al.   Life-Basel

Recognition of non-CpG repeats in Alu and ribosomal RNAs by the Z-RNA binding domain of ADAR1 induces A-Z junctions

(2021) Parker J. Nichols et al.   Nature Communications

Special Issue: A, B and Z: The Structure, Function and Genetics of Z-DNA and Z-RNA

(2021) Alan Herbert et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Structural basis of GTPase-mediated mitochondrial ribosome biogenesis and recycling

(2021) Hauke S. Hillen et al.   Nature Communications

Developments in solution-state NMR yield broader and deeper views of the dynamic ensembles of nucleic acids

(2021) Bei Liu et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Short-Range Imbalances in the AMBER Lennard-Jones Potential for (Deoxy)Ribose···Nucleobase Lone-Pair···π Contacts in Nucleic Acids

(2021) Klaudia Mráziková et al.   Journal of Chemical Information and Modeling

Z-DNA as a Touchstone for Additive Empirical Force Fields and a Refinement of the Alpha/Gamma DNA Torsions for AMBER

(2021) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

Ten things I `hate' about refinement

(2021) Pietro Roversi et al.   Acta Crystallographica Section D-Structural Biology

Integrating NMR and simulations reveals motions in the UUCG tetraloop

(2020) Sandro Bottaro et al.   NUCLEIC ACIDS RESEARCH

Short but Weak: The Z‐DNA Lone‐Pair⋅⋅⋅π Conundrum Challenges Standard Carbon Van der Waals Radii

(2020) Holger Kruse et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Analysis of translating mitoribosome reveals functional characteristics of translation in mitochondria of fungi

(2020) Yuzuru Itoh et al.   Nature Communications

Structure of the bacterial ribosome at 2 Å resolution

(2020) Zoe L Watson et al.   eLife

UUCG RNA Tetraloop as a Formidable Force-Field Challenge for MD Simulations

(2020) Klaudia Mráziková et al.   Journal of Chemical Theory and Computation

IMPROVING THE PERFORMANCE OF THE AMBER RNA FORCE FIELD BY TUNING THE HYDROGEN-BONDING INTERACTIONS

(2019) Petra Kührová et al.   Journal of Chemical Theory and Computation

Fitting Corrections to an RNA Force Field Using Experimental Data

(2019) Andrea Cesari et al.   Journal of Chemical Theory and Computation

Comment on “Evaluating Unexpectedly Short Non-covalent Distances in X-ray Crystal Structures of Proteins with Electronic Structure Analysis”

(2019) Holger Kruse et al.   Journal of Chemical Information and Modeling

Current Developments in Coot for Macromolecular Model Building of Electron Cryo‐microscopy and Crystallographic Data

(2019) Ana Casañal et al.   PROTEIN SCIENCE

Correction to “Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions”

(2019) Petra Kührová et al.   Journal of Chemical Theory and Computation

A Genetic Instruction Code Based on DNA Conformation

(2019) Alan Herbert   TRENDS IN GENETICS

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

(2018) Jiří Šponer et al.   CHEMICAL REVIEWS

Identification of receptors for UNCG and GNRA Z-turns and their occurrence in rRNA

(2018) Luigi D’Ascenzo et al.   NUCLEIC ACIDS RESEARCH

RNA force field with accuracy comparable to state-of-the-art protein force fields

(2018) Dazhi Tan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structures of two aptamers with differing ligand specificity reveal ruggedness in the functional landscape of RNA

(2018) Andrew John Knappenberger et al.   eLife

Lone pair–π interactions in biological systems: occurrence, function, and physical origin

(2017) Jiří Kozelka   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

Detect, correct, retract: How to manage incorrect structural models

(2017) Alexander Wlodawer et al.   FEBS Journal

Revised RNA Dihedral Parameters for the Amber Force Field Improve RNA Molecular Dynamics

(2017) Asaminew H. Aytenfisu et al.   Journal of Chemical Theory and Computation

Occurrence and stability of lone pair–π stacking interactions between ribose and nucleobases in functional RNAs

(2017) Mohit Chawla et al.   NUCLEIC ACIDS RESEARCH

Simultaneous NMR characterisation of multiple minima in the free energy landscape of an RNA UUCG tetraloop

(2017) Aditi N. Borkar et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

MolProbity: More and better reference data for improved all-atom structure validation

(2017) Christopher J. Williams et al.   PROTEIN SCIENCE

Correcting the record of structural publications requires joint effort of the community and journal editors

(2016) Bernhard Rupp et al.   FEBS Journal

Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies

(2016) Petra Kührová et al.   Journal of Chemical Theory and Computation

Assessing the Current State of Amber Force Field Modifications for DNA

(2016) Rodrigo Galindo-Murillo et al.   Journal of Chemical Theory and Computation

Free Energy Landscape of GAGA and UUCG RNA Tetraloops

(2016) Sandro Bottaro et al.   Journal of Physical Chemistry Letters

The RNA 3D Motif Atlas: Computational methods for extraction, organization and evaluation of RNA motifs

(2016) Lorena G. Parlea et al.   METHODS

‘Z-DNA like’ fragments in RNA: a recurring structural motif with implications for folding, RNA/protein recognition and immune response

(2016) Luigi D'Ascenzo et al.   NUCLEIC ACIDS RESEARCH

Mg2+ions: do they bind to nucleobase nitrogens?

(2016) Filip Leonarski et al.   NUCLEIC ACIDS RESEARCH

Structure and assembly model for theTrypanosoma cruzi60S ribosomal subunit

(2016) Zheng Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Revisiting GNRA and UNCG folds: U-turns versus Z-turns in RNA hairpin loops

(2016) Luigi D'Ascenzo et al.   RNA

Safeguarding Structural Data Repositories against Bad Apples

(2016) Wladek Minor et al.   STRUCTURE

Insights into Stability and Folding of GNRA and UNCG Tetraloops Revealed by Microsecond Molecular Dynamics and Well-Tempered Metadynamics

(2015) Susanta Haldar et al.   Journal of Chemical Theory and Computation

Refinement of the Sugar–Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA

(2015) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

DSSR: an integrated software tool for dissecting the spatial structure of RNA

(2015) Xiang-Jun Lu et al.   NUCLEIC ACIDS RESEARCH

Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin

(2015) George M. Giambaşu et al.   RNA

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

(2015) Christina Bergonzo et al.   RNA

An introduction to recurrent nucleotide interactions in RNA

(2014) Blake A. Sweeney et al.   Wiley Interdisciplinary Reviews-RNA

Phosphates in the Z-DNA dodecamer are flexible, but their P-SAD signal is sufficient for structure solution

(2014) Zhipu Luo et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Avoidable errors in deposited macromolecular structures: an impediment to efficient data mining

(2014) Zbigniew Dauter et al.   IUCrJ

Computer Folding of RNA Tetraloops? Are We There Yet?

(2013) Petra Kührová et al.   Journal of Chemical Theory and Computation

Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters

(2013) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

The mechanism of pseudouridine synthases from a covalent complex with RNA, and alternate specificity for U2605 versus U2604 between close homologs

(2013) Nadine Czudnochowski et al.   NUCLEIC ACIDS RESEARCH

High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations

(2013) A. A. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rethinking the term “pi-stacking”

(2012) Chelsea R. Martinez et al.   Chemical Science

High regularity of Z-DNA revealed by ultra high-resolution crystal structure at 0.55 ņ

(2011) Krzysztof Brzezinski et al.   NUCLEIC ACIDS RESEARCH

WebFR3D--a server for finding, aligning and analyzing recurrent RNA 3D motifs

(2011) A. I. Petrov et al.   NUCLEIC ACIDS RESEARCH

Prevalence of syn nucleobases in the active sites of functional RNAs

(2011) J. E. Sokoloski et al.   RNA

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

Thermodynamic characterization of naturally occurring RNA tetraloops

(2010) J. P. Sheehy et al.   RNA

High-resolution NMR structure of an RNA model system: the 14-mer cUUCGg tetraloop hairpin RNA

(2009) Senada Nozinovic et al.   NUCLEIC ACIDS RESEARCH

Frequency and isostericity of RNA base pairs

(2009) Jesse Stombaugh et al.   NUCLEIC ACIDS RESEARCH

3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures

(2008) Xiang-Jun Lu et al.   Nature Protocols

NMR and MD studies of the temperature-dependent dynamics of RNA YNMG-tetraloops

(2008) Jan Ferner et al.   NUCLEIC ACIDS RESEARCH

DNA conformations and their sequence preferences

(2008) Daniel Svozil et al.   NUCLEIC ACIDS RESEARCH

RNA backbone: Consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)

(2008) J. S. Richardson et al.   RNA