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Automated 3D structure composition for large RNAs

Nucleic acids research, 2012-08, Vol.40 (14), p.e112-e112

2012

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ElTetrado: a tool for identification and classification of tetrads and quadruplexes

BMC bioinformatics, 2020-01, Vol.21 (1), p.40-40, Article 40

2020

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

Acta biochimica Polonica, 2016-01, Vol.63 (4), p.737

2016

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

RNA (Cambridge), 2020-08, Vol.26 (8), p.982-995

2020

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RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures

RNA (Cambridge), 2015-06, Vol.21 (6), p.1066-1084

2015

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Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models

International journal of molecular sciences, 2022-08, Vol.23 (17), p.9630

2022

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

BMC bioinformatics, 2018-08, Vol.19 (1), p.304-304, Article 304

2018

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RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures

BMC bioinformatics, 2010-05, Vol.11 (1), p.231-231, Article 231

2010

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New models and algorithms for RNA pseudoknot order assignment

International journal of applied mathematics and computer science, 2020-06, Vol.30 (2)

2020

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Spiegelzymes® mirror-image hammerhead ribozymes and mirror-image DNAzymes, an alternative to siRNAs and microRNAs to cleave mRNAs in vivo?

PloS one, 2014-01, Vol.9 (1), p.e86673

2014

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RNA tertiary structure prediction using RNAComposer in CASP15

Proteins, structure, function, and bioinformatics, 2023-12, Vol.91 (12), p.1790-1799

2023

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RNApdbee 2.0: multifunctional tool for RNA structure annotation

Nucleic acids research, 2018-07, Vol.46 (W1), p.W30-W35

2018

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RNAspider: a webserver to analyze entanglements in RNA 3D structures

Nucleic acids research, 2022-07, Vol.50 (W1), p.W663-W669

2022

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Topology-based classification of tetrads and quadruplex structures

Bioinformatics, 2020-02, Vol.36 (4), p.1129-1134

2020

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New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation

Bioinformatics, 2018-04, Vol.34 (8), p.1304-1312

2018

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Entanglements of structure elements revealed in RNA 3D models

Nucleic acids research, 2021-09, Vol.49 (17), p.9625-9632

2021

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RNApdbee--a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs

Nucleic acids research, 2014-07, Vol.42 (Web Server issue), p.W368-W372

2014

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New in silico approach to assessing RNA secondary structures with non-canonical base pairs

BMC bioinformatics, 2015-09, Vol.16 (1), p.276-276, Article 276

2015

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

RNA (Cambridge), 2017-05, Vol.23 (5), p.655-672

2017

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MCQ4Structures to compute similarity of molecule structures

Central European journal of operations research, 2014-09, Vol.22 (3), p.457-473

2014

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A new molecular mechanism of RNA circularization and the microRNA sponge formation

Journal of biomolecular structure & dynamics, 2022-05, Vol.40 (7), p.3038-3045

2022

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

Nucleic acids research, 2015-07, Vol.43 (W1), p.W502-W506

2015

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The model structure of the hammerhead ribozyme formed by RNAs of reciprocal chirality

Bioscience reports, 2021-01, Vol.41 (1)

2021

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RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures

Nucleic acids research, 2008-01, Vol.36 (Database issue), p.D386-D391

2008

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RNAlyzer--novel approach for quality analysis of RNA structural models

Nucleic acids research, 2013-07, Vol.41 (12), p.5978-5990

2013

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Automated 3D structure composition for large RNAs

ElTetrado: a tool for identification and classification of tetrads and quadruplexes

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

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

RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures

Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models

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

RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures

New models and algorithms for RNA pseudoknot order assignment

Spiegelzymes® mirror-image hammerhead ribozymes and mirror-image DNAzymes, an alternative to siRNAs and microRNAs to cleave mRNAs in vivo?

RNA tertiary structure prediction using RNAComposer in CASP15

RNApdbee 2.0: multifunctional tool for RNA structure annotation

RNAspider: a webserver to analyze entanglements in RNA 3D structures

Topology-based classification of tetrads and quadruplex structures

New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation

Entanglements of structure elements revealed in RNA 3D models

RNApdbee--a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs

New in silico approach to assessing RNA secondary structures with non-canonical base pairs

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

MCQ4Structures to compute similarity of molecule structures

A new molecular mechanism of RNA circularization and the microRNA sponge formation

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

The model structure of the hammerhead ribozyme formed by RNAs of reciprocal chirality

RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures

RNAlyzer--novel approach for quality analysis of RNA structural models

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