RNA 3D structure prediction guided by independent folding of homologous sequences

Shedding light on the dark matter of the biomolecular structural universe: Progress in RNA 3D structure prediction

(2019) Fabrizio Pucci et al.   METHODS

Functional Classification and Experimental Dissection of Long Noncoding RNAs

(2018) Florian Kopp et al.   CELL

RNArchitecture: a database and a classification system of RNA families, with a focus on structural information

(2017) Pietro Boccaletto et al.   NUCLEIC ACIDS RESEARCH

Web-accessible molecular modeling with Rosetta: The Rosetta Online Server that Includes Everyone (ROSIE)

(2017) Rocco Moretti et al.   PROTEIN SCIENCE

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

(2017) Zhichao Miao et al.   RNA

3D RNA and Functional Interactions from Evolutionary Couplings

(2016) Caleb Weinreb et al.   CELL

Unravelling biological macromolecules with cryo-electron microscopy

(2016) Rafael Fernandez-Leiro et al.   NATURE

Pistol ribozyme adopts a pseudoknot fold facilitating site-specific in-line cleavage

(2016) Aiming Ren et al.   Nature Chemical Biology

Detecting circular RNAs: bioinformatic and experimental challenges

(2016) Linda Szabo et al.   NATURE REVIEWS GENETICS

SimRNAweb: a web server for RNA 3D structure modeling with optional restraints

(2016) Marcin Magnus et al.   NUCLEIC ACIDS RESEARCH

Metal Ion-Mediated Nucleobase Recognition by the ZTP Riboswitch

(2015) Jeremiah J. Trausch et al.   CHEMISTRY & BIOLOGY

An Ancient Riboswitch Class in Bacteria Regulates Purine Biosynthesis and One-Carbon Metabolism

(2015) Peter B. Kim et al.   MOLECULAR CELL

New classes of self-cleaving ribozymes revealed by comparative genomics analysis

(2015) Zasha Weinberg et al.   Nature Chemical Biology

NPDock: a web server for protein–nucleic acid docking

(2015) Irina Tuszynska et al.   NUCLEIC ACIDS RESEARCH

Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction

(2015) Eleonora De Leonardis et al.   NUCLEIC ACIDS RESEARCH

SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction

(2015) Michal J. Boniecki et al.   NUCLEIC ACIDS RESEARCH

RNA-PuzzlesRound II: assessment of RNA structure prediction programs applied to three large RNA structures

(2015) Zhichao Miao et al.   RNA

Twenty years of RNA crystallography

(2015) Eric Westhof   RNA

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

(2015) Aiming Ren et al.   Cell Reports

The Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones

(2014) Thomas R. Cech et al.   CELL

A Disconnect between High-Affinity Binding and Efficient Regulation by Antifolates and Purines in the Tetrahydrofolate Riboswitch

(2014) Jeremiah J. Trausch et al.   CHEMISTRY & BIOLOGY

Crystal structure of a c-di-AMP riboswitch reveals an internally pseudo-dimeric RNA

(2014) C. P. Jones et al.   EMBO JOURNAL

Structural insights into recognition of c-di-AMP by the ydaO riboswitch

(2014) Ang Gao et al.   Nature Chemical Biology

c-di-AMP binds the ydaO riboswitch in two pseudo-symmetry–related pockets

(2014) Aiming Ren et al.   Nature Chemical 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

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction

(2013) Tomasz Puton et al.   NUCLEIC ACIDS RESEARCH

RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction

(2012) J. A. Cruz et al.   RNA

DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking

(2011) Irina Tuszynska et al.   BMC BIOINFORMATICS

Structural basis of differential ligand recognition by two classes of bis-(3'-5')-cyclic dimeric guanosine monophosphate-binding riboswitches

(2011) K. D. Smith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Atomic accuracy in predicting and designing noncanonical RNA structure

(2010) Rhiju Das et al.   NATURE METHODS

On the significance of an RNA tertiary structure prediction

(2010) C. E. Hajdin et al.   RNA

The amazing world of bacterial structured RNAs

(2010) Eric Westhof   GENOME BIOLOGY

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

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

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments

(2008) Stefan E. Seemann et al.   NUCLEIC ACIDS RESEARCH