Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions

Entanglements of structure elements revealed in RNA 3D models

(2021) Mariusz Popenda et al.   NUCLEIC ACIDS RESEARCH

RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers

(2020) Zhichao Miao et al.   RNA

Scalable molecular dynamics on CPU and GPU architectures with NAMD

(2020) James C. Phillips et al.   JOURNAL OF CHEMICAL PHYSICS

Transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to animals: an updated review

(2020) Sina Salajegheh Tazerji et al.   Journal of Translational Medicine

RNAthor – fast, accurate normalization, visualization and statistical analysis of RNA probing data resolved by capillary electrophoresis

(2020) Julita Gumna et al.   PLoS One

Advances in RNA 3D Structure Modeling Using Experimental Data

(2020) Bing Li et al.   Frontiers in Genetics

QRNAS: software tool for refinement of nucleic acid structures

(2019) Juliusz Stasiewicz et al.   BMC STRUCTURAL BIOLOGY

RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools

(2019) Marcin Magnus et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Maciej Antczak et al.   BMC BIOINFORMATICS

Coupling Between Conformational Dynamics and Catalytic Function at the Active Site of the Lead-Dependent Ribozyme

(2018) Neil A White et al.   RNA

Barnaba: software for analysis of nucleic acid structures and trajectories

(2018) Sandro Bottaro et al.   RNA

MolProbity: More and better reference data for improved all-atom structure validation

(2017) Christopher J. Williams et al.   PROTEIN SCIENCE

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

(2017) Zhichao Miao et al.   RNA

OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive

(2017) Jasmine Y. Young et al.   STRUCTURE

Validation of Structures in the Protein Data Bank

(2017) Swanand Gore et al.   STRUCTURE

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

(2016) Maciej Antczak et al.   ACTA BIOCHIMICA POLONICA

Combined automated NOE assignment and structure calculation with CYANA

(2015) Peter Güntert et al.   JOURNAL OF BIOMOLECULAR NMR

RNAssess—a web server for quality assessment of RNA 3D structures

(2015) Piotr Lukasiak 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

A crystallographic perspective on sharing data and knowledge

(2014) Ian J. Bruno et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

(2014) Xiaojun Xu et al.   PLoS One

MCQ4Structures to compute similarity of molecule structures

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

Statistical quality indicators for electron-density maps

(2012) Ian J. Tickle   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Automated 3D structure composition for large RNAs

(2012) Mariusz Popenda et al.   NUCLEIC ACIDS RESEARCH

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

(2012) J. A. Cruz et al.   RNA

Automated and fast building of three-dimensional RNA structures

(2012) Yunjie Zhao et al.   Scientific Reports

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

(2011) Magdalena Rother et al.   NUCLEIC ACIDS RESEARCH

Atomic accuracy in predicting and designing noncanonical RNA structure

(2010) Rhiju Das et al.   NATURE METHODS

Crystallographic model quality at a glance

(2009) Ludmila Urzhumtseva et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters

(2009) M. A. Jonikas et al.   RNA

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

(2009) M. Parisien et al.   RNA

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

(2008) Marc Parisien et al.   NATURE

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

(2008) F. Ding et al.   RNA