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RNAsolo: a repository of cleaned PDB-derived RNA 3D structures

Bioinformatics, 2022-07, Vol.38 (14), p.3668-3670

2022

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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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Knotted artifacts in predicted 3D RNA structures

PLoS computational biology, 2024-06, Vol.20 (6), p.e1011959

2024

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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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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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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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A Survey on Online Judge Systems and Their Applications

ACM computing surveys, 2018-01, Vol.51 (1), p.1-34

2018

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Toward Increasing the Credibility of RNA Design

Methods in molecular biology (Clifton, N.J.), 2025, Vol.2847, p.137

2025

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High-quality, customizable heuristics for RNA 3D structure alignment

Bioinformatics (Oxford, England), 2023-05, Vol.39 (5)

2023

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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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RNAhugs web server for customized 3D RNA structure alignment

Nucleic acids research, 2024-07, Vol.52 (W1), p.W348-W353

2024

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Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions

RNA (Cambridge), 2022-02, Vol.28 (2), p.250-262

2022

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Machine learning for RNA 2D structure prediction benchmarked on experimental data

Briefings in bioinformatics, 2023-05, Vol.24 (3)

2023

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Building the library of RNA 3D nucleotide conformations using the clustering approach

International journal of applied mathematics and computer science, 2015-09, Vol.25 (3), p.689-700

2015

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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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RNAloops: a database of RNA multiloops

Bioinformatics, 2022-09, Vol.38 (17), p.4200-4205

2022

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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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RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools

Nucleic acids research, 2020-01, Vol.48 (2), p.576

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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New prediction categories in CASP15

Proteins, structure, function, and bioinformatics, 2023-12, Vol.91 (12), p.1550-1557

2023

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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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RNAvista: a webserver to assess RNA secondary structures with non-canonical base pairs

Bioinformatics, 2019-01, Vol.35 (1), p.152-155

2019

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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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RNAsolo: a repository of cleaned PDB-derived RNA 3D structures

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

Knotted artifacts in predicted 3D RNA structures

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

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

New models and algorithms for RNA pseudoknot order assignment

A Survey on Online Judge Systems and Their Applications

Toward Increasing the Credibility of RNA Design

High-quality, customizable heuristics for RNA 3D structure alignment

RNA tertiary structure prediction using RNAComposer in CASP15

RNAhugs web server for customized 3D RNA structure alignment

Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions

Machine learning for RNA 2D structure prediction benchmarked on experimental data

Building the library of RNA 3D nucleotide conformations using the clustering approach

RNApdbee 2.0: multifunctional tool for RNA structure annotation

RNAloops: a database of RNA multiloops

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

RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools

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

New prediction categories in CASP15

Entanglements of structure elements revealed in RNA 3D models

RNAvista: a webserver to assess RNA secondary structures with non-canonical base pairs

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

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