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

scholarly article by Jun Li published in November 2018

RNA3DCNN: Local and global quality assessments of RNA 3D structures using 3D deep convolutional neural networks is …
instance of (P31):
scholarly articleQ13442814

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P8978DBLP publication IDjournals/ploscb/LiZWLGZW18
P356DOI10.1371/JOURNAL.PCBI.1006514
P932PMC publication ID6258470
P698PubMed publication ID30481171

P50authorJian ZhangQ59678165
P2093author name stringWei Wang
Wei Zhu
Jun Wang
Jun Li
Wenfei Li
Sheng Gong
P2860cites workA probabilistic model of RNA conformational spaceQ21145357
The rise of regulatory RNAQ22121998
Turning limited experimental information into 3D models of RNAQ24630208
Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filtersQ24647503
iFoldRNA: three-dimensional RNA structure prediction and foldingQ24658133
Automated de novo prediction of native-like RNA tertiary structuresQ24673712
The noncoding RNA revolution-trashing old rules to forge new onesQ26851952
Mastering the game of Go with deep neural networks and tree searchQ28005460
Long non-coding RNAs: insights into functionsQ28131764
The MC-Fold and MC-Sym pipeline infers RNA structure from sequence dataQ28271703
An improved protein decoy set for testing energy functions for protein structure prediction.Q30333352
Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluationQ30402159
3D deep convolutional neural networks for amino acid environment similarity analysisQ30403066
Sequence to Structure (S2S): display, manipulate and interconnect RNA data from sequence to structureQ30990184
A coarse-grained model with implicit salt for RNAs: predicting 3D structure, stability and salt effect.Q51038351
RNA fragment modeling with a nucleobase discrete-state modelQ83776001
HiRE-RNA: A High Resolution Coarse-Grained Energy Model for RNAQ84959270
A nucleotide-level coarse-grained model of RNAQ88127110
Development and evaluation of a deep learning model for protein-ligand binding affinity predictionQ88661460
MANIP: an interactive tool for modelling RNA.Q31412438
RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozymeQ33364669
Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levelsQ33609575
Atomic accuracy in predicting and designing noncanonical RNA structureQ33789129
Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learningQ34487019
RNA2D3D: a program for generating, viewing, and comparing 3-dimensional models of RNAQ34768823
ModeRNA: a tool for comparative modeling of RNA 3D structureQ35017843
Vfold: a web server for RNA structure and folding thermodynamics predictionQ35249784
RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structuresQ35621422
An enumerative stepwise ansatz enables atomic-accuracy RNA loop modelingQ35651055
3dRNAscore: a distance and torsion angle dependent evaluation function of 3D RNA structuresQ35656687
RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure predictionQ35853409
Automated and fast building of three-dimensional RNA structuresQ36316650
Predicting 3D Structure, Flexibility, and Stability of RNA Hairpins in Monovalent and Divalent Ion SolutionsQ36429548
Predicting effects of noncoding variants with deep learning-based sequence modelQ36621822
RNA in unexpected places: long non-coding RNA functions in diverse cellular contextsQ36855920
Prediction of geometrically feasible three-dimensional structures of pseudoknotted RNA through free energy estimationQ37426607
ProQ3D: improved model quality assessments using deep learningQ38374451
DeepSite: Protein binding site predictor using 3D-convolutional neural networks.Q38748498
Protein-Ligand Scoring with Convolutional Neural Networks.Q38860867
Optimization of RNA 3D structure prediction using evolutionary restraints of nucleotide-nucleotide interactions from direct coupling analysis.Q40950675
Coarse-grained prediction of RNA loop structures.Q41329375
Mastering the game of Go without human knowledgeQ42209359
RNA splicing. The human splicing code reveals new insights into the genetic determinants of diseaseQ42558500
Physics-based de novo prediction of RNA 3D structures.Q42712420
All-atom knowledge-based potential for RNA structure prediction and assessmentQ45783105
Solving the quantum many-body problem with artificial neural networks.Q45948562
Hierarchical Assembly of RNA Three-Dimensional Structures Based on Loop Templates.Q47234232
Predicting RNA Structure with Vfold.Q49289634
Non-coding RNA networks in cancer.Q49689803
P275copyright licenseCreative Commons Attribution 4.0 InternationalQ20007257
P6216copyright statuscopyrightedQ50423863
P433issue11
P407language of work or nameEnglishQ1860
P921main subjectmolecular biologyQ7202
convolutional neural networkQ17084460
P304page(s)e1006514
P577publication date2018-11-01
P1433published inPLOS Computational BiologyQ2635829
P1476titleRNA3DCNN: Local and global quality assessments of RNA 3D structures using 3D deep convolutional neural networks
P478volume14

Reverse relations

cites work (P2860)
Q90123830Energy-based graph convolutional networks for scoring protein docking models
Q91678594RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools

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