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

New functionality of RNAComposer: an application to shape the axis of miR160 precursor structure

(2016) Maciej Antczak et al.   ACTA BIOCHIMICA POLONICA

Computational modeling of RNA 3D structures and interactions

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

Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules

(2016) Hahnbeom Park et al.   Journal of Chemical Theory and Computation

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

(2016) Marcin Magnus et al.   NUCLEIC ACIDS RESEARCH

Blind tests of RNA nearest-neighbor energy prediction

(2016) Fang-Chieh Chou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Critical assessment of methods of protein structure prediction: Progress and new directions in round XI

(2016) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

RNA structure through multidimensional chemical mapping

(2016) Siqi Tian et al.   QUARTERLY REVIEWS OF BIOPHYSICS

iFoldRNA v2: folding RNA with constraints: Fig. 1.

(2015) Andrey Krokhotin et al.   BIOINFORMATICS

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

Crystal structure of the Varkud satellite ribozyme

(2015) Nikolai B Suslov et al.   Nature Chemical Biology

The I-TASSER Suite: protein structure and function prediction

(2015) Jianyi Yang et al.   NATURE METHODS

NPDock: a web server for protein–nucleic acid docking

(2015) Irina Tuszynska et al.   NUCLEIC ACIDS RESEARCH

3dRNAscore: a distance and torsion angle dependent evaluation function of 3D RNA structures

(2015) Jian Wang 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

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

(2015) Aiming Ren et al.   Cell Reports

Consistent global structures of complex RNA states through multidimensional chemical mapping

(2015) Clarence Yu Cheng et al.   eLife

Standardization of RNA Chemical Mapping Experiments

(2014) Wipapat Kladwang et al.   BIOCHEMISTRY

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

RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP)

(2014) Nathan A Siegfried et al.   NATURE METHODS

RNApdbee—a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs

(2014) Maciej Antczak et al.   NUCLEIC ACIDS RESEARCH

Vfold: A Web Server for RNA Structure and Folding Thermodynamics Prediction

(2014) Xiaojun Xu et al.   PLoS One

Structural basis for diversity in the SAM clan of riboswitches

(2014) J. J. Trausch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MCQ4Structures to compute similarity of molecule structures

(2013) Tomasz Zok et al.   Central European Journal of Operations Research

Riboswitches in eubacteria sense the second messenger c-di-AMP

(2013) James W Nelson et al.   Nature Chemical Biology

Atomic-Accuracy Prediction of Protein Loop Structures through an RNA-Inspired Ansatz

(2013) Rhiju Das   PLoS One

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

Retrotransposon Ty1 RNA contains a 5'-terminal long-range pseudoknot required for efficient reverse transcription

(2013) Q. Huang et al.   RNA

An RNA Mapping DataBase for curating RNA structure mapping experiments

(2012) Pablo Cordero et al.   BIOINFORMATICS

Automated prediction of three-way junction topological families in RNA secondary structures

(2012) Alexis Lamiable et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Discrete Molecular Dynamics: An Efficient And Versatile Simulation Method For Fine Protein Characterization

(2012) David Shirvanyants et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Three-dimensional RNA structure refinement by hydroxyl radical probing

(2012) Feng Ding et al.   NATURE METHODS

Rfam 11.0: 10 years of RNA families

(2012) Sarah W. Burge et al.   NUCLEIC ACIDS RESEARCH

Automated 3D structure composition for large RNAs

(2012) Mariusz Popenda et al.   NUCLEIC ACIDS RESEARCH

YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops

(2012) N. J. Baird et al.   RNA

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

(2012) J. A. Cruz et al.   RNA

ModeRNA server: an online tool for modeling RNA 3D structures

(2011) M. Rother et al.   BIOINFORMATICS

ModeRNA: a tool for comparative modeling of RNA 3D structure

(2011) Magdalena Rother et al.   NUCLEIC ACIDS RESEARCH

Bacterial aptamers that selectively bind glutamine

(2011) Tyler D. Ames et al.   RNA Biology

Discrete molecular dynamics

(2011) Elizabeth A. Proctor et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures

(2010) Mariusz Popenda et al.   BMC BIOINFORMATICS

Do the hairpin and VS ribozymes share a common catalytic mechanism based on general acid-base catalysis? A critical assessment of available experimental data

(2010) T. J. Wilson et al.   RNA

Free State Conformational Sampling of the SAM-I Riboswitch Aptamer Domain

(2010) Colby D. Stoddard et al.   STRUCTURE

MolProbity: all-atom structure validation for macromolecular crystallography

(2009) Vincent B. Chen et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Native-like RNA Tertiary Structures Using a Sequence-Encoded Cleavage Agent and Refinement by Discrete Molecular Dynamics

(2009) Costin M. Gherghe et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Formation of an active site in trans by interaction of two complete Varkud Satellite ribozymes

(2009) J. Ouellet et al.   RNA

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

(2009) M. Parisien et al.   RNA

iFoldRNA: three-dimensional RNA structure prediction and folding

(2008) Shantanu Sharma et al.   BIOINFORMATICS

Rfam: updates to the RNA families database

(2008) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH

Ab initio RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms

(2008) F. Ding et al.   RNA

Ab Initio Folding of Proteins with All-Atom Discrete Molecular Dynamics

(2008) Feng Ding et al.   STRUCTURE