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

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

(2015) Rajendra Kumar et al.   BIOINFORMATICS

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

Interplay of the Bacterial Ribosomal A-Site, S12 Protein Mutations and Paromomycin Binding: A Molecular Dynamics Study

(2014) Joanna Panecka et al.   PLoS One

Bioinformatics and Molecular Dynamics Simulation Study of L1 Stalk Non-Canonical rRNA Elements: Kink-Turns, Loops, and Tetraloops

(2013) Miroslav Krepl et al.   JOURNAL OF PHYSICAL CHEMISTRY B

RNAmap2D – calculation, visualization and analysis of contact and distance maps for RNA and protein-RNA complex structures

(2012) Michal J Pietal et al.   BMC BIOINFORMATICS

Magnesium Fluctuations Modulate RNA Dynamics in the SAM-I Riboswitch

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

MODOMICS: a database of RNA modification pathways—2013 update

(2012) Magdalena A. Machnicka et al.   NUCLEIC ACIDS RESEARCH

Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA

(2011) Elizabeth J. Denning et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

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

Structures of the Bacterial Ribosome in Classical and Hybrid States of tRNA Binding

(2011) J. A. Dunkle et al.   SCIENCE

Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels

(2010) F. Jossinet et al.   BIOINFORMATICS

Computational approaches to 3D modeling of RNA

(2010) Christian Laing et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Connecting Energy Landscapes with Experimental Rates for Aminoacyl-tRNA Accommodation in the Ribosome

(2010) Paul C. Whitford et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The RNA backbone plays a crucial role in mediating the intrinsic stability of the GpU dinucleotide platform and the GpUpA/GpA miniduplex

(2010) Xiang-Jun Lu et al.   NUCLEIC ACIDS RESEARCH

The RNA modification database, RNAMDB: 2011 update

(2010) W. A. Cantara et al.   NUCLEIC ACIDS RESEARCH

VARNA: Interactive drawing and editing of the RNA secondary structure

(2009) Kévin Darty et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Conformational analysis of nucleic acids revisited: Curves+

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

Simulating RNA Folding Kinetics on Approximated Energy Landscapes

(2008) Xinyu Tang et al.   JOURNAL OF MOLECULAR 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

From knotted to nested RNA structures: A variety of computational methods for pseudoknot removal

(2008) S. Smit et al.   RNA