Geometric deep learning of RNA structure

Improved protein structure prediction using potentials from deep learning

(2020) Andrew W. Senior et al.   NATURE

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

(2020) Zhichao Miao et al.   RNA

Evaluating DCA-based method performances for RNA contact prediction by a well-curated dataset

(2020) Fabrizio Pucci et al.   RNA

Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures

(2020) Kalli Kappel et al.   NATURE METHODS

FARFAR2: Improved De Novo Rosetta Prediction of Complex Global RNA Folds

(2020) Andrew Martin Watkins et al.   STRUCTURE

Rfam 14: expanded coverage of metagenomic, viral and microRNA families

(2020) Ioanna Kalvari et al.   NUCLEIC ACIDS RESEARCH

Hierarchical, rotation‐equivariant neural networks to select structural models of protein complexes

(2020) Stephan Eismann et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

End-to-End Differentiable Learning of Protein Structure

(2019) Mohammed AlQuraishi   Cell Systems

Crystal structure of an adenovirus virus-associated RNA

(2019) Iris V. Hood et al.   Nature Communications

Distance-based protein folding powered by deep learning

(2019) Jinbo Xu   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Boltzmann generators: Sampling equilibrium states of many-body systems with deep learning

(2019) Frank Noé et al.   SCIENCE

Structural basis of amino acid surveillance by higher-order tRNA-mRNA interactions

(2019) Shuang Li et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

High-affinity recognition of specific tRNAs by an mRNA anticodon-binding groove

(2019) Krishna C. Suddala et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Principles for targeting RNA with drug-like small molecules

(2018) Katherine Deigan Warner et al.   NATURE REVIEWS DRUG DISCOVERY

Tandem riboswitches form a natural Boolean logic gate to control purine metabolism in bacteria

(2018) Madeline E Sherlock et al.   eLife

RNA3DCNN: Local and global quality assessments of RNA 3D structures using 3D deep convolutional neural networks

(2018) Jun Li et al.   PLoS Computational Biology

Protein–Ligand Scoring with Convolutional Neural Networks

(2017) Matthew Ragoza et al.   Journal of Chemical Information and Modeling

ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost

(2017) J. S. Smith et al.   Chemical Science

Transcending the prediction paradigm: novel applications of SHAPE to RNA function and evolution

(2016) Katrina M. Kutchko et al.   Wiley Interdisciplinary Reviews-RNA

Structural Analysis of Adenovirus VAI RNA Defines the Mechanism of Inhibition of PKR

(2015) Katherine Launer-Felty et al.   BIOPHYSICAL JOURNAL

Deep learning

(2015) Yann LeCun et al.   NATURE

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

T box riboswitches in Actinobacteria: Translational regulation via novel tRNA interactions

(2015) Anna V. Sherwood et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The purine riboswitch as a model system for exploring RNA biology and chemistry

(2014) Ely B. Porter et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

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

(2014) Thomas R. Cech et al.   CELL

Direct Evaluation of tRNA Aminoacylation Status by the T-Box Riboswitch Using tRNA-mRNA Stacking and Steric Readout

(2014) Jinwei Zhang et al.   MOLECULAR CELL

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era

(2013) H. Kamisetty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

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

(2011) Emidio Capriotti et al.   BIOINFORMATICS

Protein 3D Structure Computed from Evolutionary Sequence Variation

(2011) Debora S. Marks et al.   PLoS One

PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta

(2010) S. Chaudhury et al.   BIOINFORMATICS

Atomic accuracy in predicting and designing noncanonical RNA structure

(2010) Rhiju Das et al.   NATURE METHODS

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

(2009) M. Parisien et al.   RNA