QRNAS: software tool for refinement of nucleic acid structures

Computational modeling of RNA 3D structure based on experimental data

(2019) Almudena Ponce-Salvatierra et al.   BIOSCIENCE REPORTS

RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures

(2018) Maciej Antczak et al.   BMC BIOINFORMATICS

Critical assessment of methods of protein structure prediction (CASP)-Round XII

(2017) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2017) Zhichao Miao et al.   RNA

Coarse-grained modeling of RNA 3D structure

(2016) Wayne K. Dawson et al.   METHODS

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

(2016) Marcin Magnus 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

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

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

(2014) Xiaojun Xu et al.   PLoS One

Structural Principles of RNA Catalysis in a 2′–5′ Lariat-Forming Ribozyme

(2013) Teresa Carlomagno et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The Impact of Aminoglycosides on the Dynamics of Translation Elongation

(2013) Albert Tsai et al.   Cell Reports

Solution Structure of the Dickerson DNA Dodecamer Containing a Single Ribonucleotide

(2012) Eugene F. DeRose et al.   BIOCHEMISTRY

Fluoride ion encapsulation by Mg2+ ions and phosphates in a fluoride riboswitch

(2012) Aiming Ren et al.   NATURE

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

(2012) J. A. Cruz et al.   RNA

An overview of the Amber biomolecular simulation package

(2012) Romelia Salomon-Ferrer et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

All-atom knowledge-based potential for RNA structure prediction and assessment

(2011) Emidio Capriotti et al.   BIOINFORMATICS

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

(2011) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

An equilibrium-dependent retroviral mRNA switch regulates translational recoding

(2011) Brian Houck-Loomis et al.   NATURE

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

(2011) Magdalena Rother et al.   NUCLEIC ACIDS RESEARCH

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

Atomic accuracy in predicting and designing noncanonical RNA structure

(2010) Rhiju Das et al.   NATURE METHODS

MolProbity: all-atom structure validation for macromolecular crystallography

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

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

Hydrogen-bond network and local structure of liquid water: An atoms-in-molecules perspective

(2008) Haigang Lu et al.   JOURNAL OF CHEMICAL PHYSICS

The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data

(2008) Marc Parisien et al.   NATURE