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

Protein–Ligand Scoring with Convolutional Neural Networks

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

Mastering the game of Go without human knowledge

(2017) David Silver et al.   NATURE

Learning phase transitions by confusion

(2017) Evert P. L. van Nieuwenburg et al.   Nature Physics

Machine learning phases of matter

(2017) Juan Carrasquilla et al.   Nature Physics

Optimization of RNA 3D structure prediction using evolutionary restraints of nucleotide–nucleotide interactions from direct coupling analysis

(2017) Jian Wang et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Zhichao Miao et al.   RNA

Solving the quantum many-body problem with artificial neural networks

(2017) Giuseppe Carleo et al.   SCIENCE

Mastering the game of Go with deep neural networks and tree search

(2016) David Silver et al.   NATURE

Predicting 3D Structure, Flexibility, and Stability of RNA Hairpins in Monovalent and Divalent Ion Solutions

(2015) Ya-Zhou Shi et al.   BIOPHYSICAL JOURNAL

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

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

(2015) Jian Wang 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

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

(2014) Thomas R. Cech et al.   CELL

A nucleotide-level coarse-grained model of RNA

(2014) Petr Šulc et al.   JOURNAL OF CHEMICAL PHYSICS

The rise of regulatory RNA

(2014) Kevin V. Morris et al.   NATURE REVIEWS GENETICS

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

(2014) Xiaojun Xu et al.   PLoS One

The human splicing code reveals new insights into the genetic determinants of disease

(2014) H. Y. Xiong et al.   SCIENCE

RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts

(2013) Sarah Geisler et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

RNA2D3D: A program for Generating, Viewing, and Comparing 3-Dimensional Models of RNA

(2012) Hugo M. Martinez et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

RNA fragment modeling with a nucleobase discrete-state model

(2012) Jian Zhang et al.   PHYSICAL REVIEW E

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

(2012) J. A. Cruz et al.   RNA

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

(2011) Emidio Capriotti et al.   BIOINFORMATICS

Physics-Based De Novo Prediction of RNA 3D Structures

(2011) Song Cao et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

(2011) Magdalena Rother et al.   NUCLEIC ACIDS RESEARCH

An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling

(2011) P. Sripakdeevong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation

(2011) J. Bernauer et al.   RNA

Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels

(2010) F. Jossinet et al.   BIOINFORMATICS

HiRE-RNA: A High Resolution Coarse-Grained Energy Model for RNA

(2010) Samuela Pasquali et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Atomic accuracy in predicting and designing noncanonical RNA structure

(2010) Rhiju Das et al.   NATURE METHODS

Turning limited experimental information into 3D models of RNA

(2010) S. C. Flores et al.   RNA

Long non-coding RNAs: insights into functions

(2009) Tim R. Mercer et al.   NATURE REVIEWS GENETICS

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

(2009) M. A. Jonikas et al.   RNA

Prediction of geometrically feasible three-dimensional structures of pseudoknotted RNA through free energy estimation

(2009) J. Zhang et al.   RNA

A Probabilistic Model of RNA Conformational Space

(2009) Jes Frellsen et al.   PLoS Computational Biology

iFoldRNA: three-dimensional RNA structure prediction and folding

(2008) Shantanu Sharma et al.   BIOINFORMATICS

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

(2008) Marc Parisien et al.   NATURE