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RNAstructure: software for RNA secondary structure prediction and analysis

BMC bioinformatics, 2010-03, Vol.11 (1), p.129-129, Article 129

2010

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How to benchmark RNA secondary structure prediction accuracy

Methods (San Diego, Calif.), 2019-06, Vol.162-163, p.60-67

Mathews, David H.

2019

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NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure

Nucleic acids research, 2010-01, Vol.38 (Database issue), p.D280-D282

2010

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LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search

Bioinformatics, 2019-07, Vol.35 (14), p.i295-i304

2019

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TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs

Nucleic acids research, 2017-11, Vol.45 (20), p.11570-11581

2017

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RNAstructure: Web servers for RNA secondary structure prediction and analysis

Nucleic acids research, 2013-07, Vol.41 (Web Server issue), p.W471-W474

2013

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LinearPartition: linear-time approximation of RNA folding partition function and base-pairing probabilities

Bioinformatics (Oxford, England), 2020-07, Vol.36 (Supplement_1), p.i258-i267

2020

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ProbKnot: fast prediction of RNA secondary structure including pseudoknots

RNA (Cambridge), 2010-10, Vol.16 (10), p.1870-1880

2010

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LazySampling and LinearSampling: fast stochastic sampling of RNA secondary structure with applications to SARS-CoV-2

Nucleic acids research, 2023-01, Vol.51 (2), p.e7-e7

2023

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Nearest neighbor rules for RNA helix folding thermodynamics: improved end effects

Nucleic acids research, 2022-05, Vol.50 (9), p.5251-5262

2022

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CRISPR-Cas9-based mutagenesis frequently provokes on-target mRNA misregulation

Nature communications, 2019-09, Vol.10 (1), p.4056-10, Article 4056

2019

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Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures

RNA (Cambridge), 2016-12, Vol.22 (12), p.1808-1818

2016

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Accurate SHAPE-directed RNA structure determination

Proceedings of the National Academy of Sciences - PNAS, 2009-01, Vol.106 (1), p.97-102

2009

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Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots

Proceedings of the National Academy of Sciences - PNAS, 2013-04, Vol.110 (14), p.5498-5503

2013

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Prediction of RNA secondary structure by free energy minimization

Current opinion in structural biology, 2006-06, Vol.16 (3), p.270-278

2006

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RNA Secondary Structure Analysis Using RNAstructure

Current Protocols in Bioinformatics, 2014-06, Vol.46 (1), p.12.6.1-12.6.25

Mathews, David H.

2014

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mRNAs and lncRNAs intrinsically form secondary structures with short end-to-end distances

Nature communications, 2018-10, Vol.9 (1), p.4328-11, Article 4328

2018

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Improved RNA secondary structure prediction by maximizing expected pair accuracy

RNA (Cambridge), 2009-10, Vol.15 (10), p.1805-1813

2009

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Revolutions in RNA Secondary Structure Prediction

Journal of molecular biology, 2006-06, Vol.359 (3), p.526-532

Mathews, David H.

2006

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TurboFold: iterative probabilistic estimation of secondary structures for multiple RNA sequences

BMC bioinformatics, 2011-04, Vol.12 (1), p.108-108, Article 108

2011

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Making ends meet: New functions of mRNA secondary structure

Wiley interdisciplinary reviews. RNA, 2021-03, Vol.12 (2), p.e1611-n/a

2021

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A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control

Nature communications, 2022-01, Vol.13 (1), p.199-199, Article 199

2022

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Pre-mRNA splicing factor U2AF2 recognizes distinct conformations of nucleotide variants at the center of the pre-mRNA splice site signal

Nucleic acids research, 2022-05, Vol.50 (9), p.5299-5312

2022

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A riboswitch separated from its ribosome-binding site still regulates translation

Nucleic acids research, 2023-03, Vol.51 (5), p.2464-2484

2023

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Incorporating Chemical Modification Constraints into a Dynamic Programming Algorithm for Prediction of RNA Secondary Structure

Proceedings of the National Academy of Sciences - PNAS, 2004-05, Vol.101 (19), p.7287-7292

2004

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RNAstructure: software for RNA secondary structure prediction and analysis

How to benchmark RNA secondary structure prediction accuracy

NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure

LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search

TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs

RNAstructure: Web servers for RNA secondary structure prediction and analysis

LinearPartition: linear-time approximation of RNA folding partition function and base-pairing probabilities

ProbKnot: fast prediction of RNA secondary structure including pseudoknots

LazySampling and LinearSampling: fast stochastic sampling of RNA secondary structure with applications to SARS-CoV-2

Nearest neighbor rules for RNA helix folding thermodynamics: improved end effects

CRISPR-Cas9-based mutagenesis frequently provokes on-target mRNA misregulation

Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures

Accurate SHAPE-directed RNA structure determination

Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots

Prediction of RNA secondary structure by free energy minimization

RNA Secondary Structure Analysis Using RNAstructure

mRNAs and lncRNAs intrinsically form secondary structures with short end-to-end distances

Improved RNA secondary structure prediction by maximizing expected pair accuracy

Revolutions in RNA Secondary Structure Prediction

TurboFold: iterative probabilistic estimation of secondary structures for multiple RNA sequences

Making ends meet: New functions of mRNA secondary structure

A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control

Pre-mRNA splicing factor U2AF2 recognizes distinct conformations of nucleotide variants at the center of the pre-mRNA splice site signal

A riboswitch separated from its ribosome-binding site still regulates translation

Incorporating Chemical Modification Constraints into a Dynamic Programming Algorithm for Prediction of RNA Secondary Structure

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