Barnaba: software for analysis of nucleic acid structures and trajectories

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

(2018) Jiří Šponer et al.   CHEMICAL REVIEWS

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

Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations

(2018) Sandro Bottaro et al.   Science Advances

Predicting the Kinetics of RNA Oligonucleotides Using Markov State Models

(2017) Giovanni Pinamonti et al.   Journal of Chemical Theory and Computation

Predicting RNA Structures via a Simple van der Waals Correction to an All-Atom Force Field

(2017) Changwon Yang et al.   Journal of Chemical Theory and Computation

A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs

(2017) Simón Poblete et al.   NUCLEIC ACIDS RESEARCH

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

(2017) Zhichao Miao et al.   RNA

Computational modeling of RNA 3D structures and interactions

(2016) Wayne K Dawson et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

(2016) Petra Kührová 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

RNA folding pathways in stop motion

(2016) Sandro Bottaro et al.   NUCLEIC ACIDS RESEARCH

do_x3dna: a tool to analyze structural fluctuations of dsDNA or dsRNA from molecular dynamics simulations: Fig. 1.

(2015) Rajendra Kumar et al.   BIOINFORMATICS

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

(2015) Robert T. McGibbon et al.   BIOPHYSICAL JOURNAL

Stacking in RNA: NMR of Four Tetramers Benchmark Molecular Dynamics

(2015) David E. Condon 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

Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments

(2015) Giovanni Pinamonti et al.   NUCLEIC ACIDS RESEARCH

MINT: software to identify motifs and short-range interactions in trajectories of nucleic acids

(2015) Anna Górska et al.   NUCLEIC ACIDS RESEARCH

ENCORE: Software for Quantitative Ensemble Comparison

(2015) Matteo Tiberti et al.   PLoS Computational Biology

ClaRNA: a classifier of contacts in RNA 3D structures based on a comparative analysis of various classification schemes

(2014) Tomasz Waleń et al.   NUCLEIC ACIDS RESEARCH

The role of nucleobase interactions in RNA structure and dynamics

(2014) Sandro Bottaro et al.   NUCLEIC ACIDS RESEARCH

Elastic network models capture the motions apparent within ensembles of RNA structures

(2014) M. T. Zimmermann et al.   RNA

PLUMED 2: New feathers for an old bird

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

Elastic Network Models of Nucleic Acids Flexibility

(2013) Piotr Setny et al.   Journal of Chemical Theory and Computation

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots

(2013) C. E. Hajdin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

(2011) Naveen Michaud-Agrawal et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Ionic strength-dependent persistence lengths of single-stranded RNA and DNA

(2011) H. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

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

(2009) Senada Nozinovic et al.   NUCLEIC ACIDS RESEARCH

Conformational analysis of nucleic acids revisited: Curves+

(2009) R. Lavery et al.   NUCLEIC ACIDS RESEARCH

New metrics for comparing and assessing discrepancies between RNA 3D structures and models

(2009) M. Parisien et al.   RNA

A Probabilistic Model of RNA Conformational Space

(2009) Jes Frellsen et al.   PLoS Computational Biology

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

Correspondences between low-energy modes in enzymes: Dynamics-based alignment of enzymatic functional families

(2008) Andrea Zen et al.   PROTEIN SCIENCE

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

(2008) J. S. Richardson et al.   RNA