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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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Data-informed reparameterization of modified RNA and the effect of explicit water models: application to pseudouridine and derivatives

Journal of computer-aided molecular design, 2022-03, Vol.36 (3), p.205-224

2022

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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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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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Mutations in human AID differentially affect its ability to deaminate cytidine and 5-methylcytidine in ssDNA substrates in vitro

Scientific reports, 2017-06, Vol.7 (1), p.3873-16, Article 3873

2017

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Structural Stability of the Anticodon Stem Loop Domains of the Unmodified Yeast and Escherichia coli tRNAPhe: Differing Views from Different Force Fields

ACS omega, 2019-02, Vol.4 (2), p.3029-3044

2019

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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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How bioinformatics resources work with G4 RNAs

Briefings in bioinformatics, 2021-05, Vol.22 (3)

2021

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Computational and NMR studies of RNA duplexes with an internal pseudouridine-adenosine base pair

Scientific reports, 2019-11, Vol.9 (1), p.16278-13, Article 16278

2019

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Predicting nearest neighbor free energies of modified RNA with LIE: results for pseudouridine and N1-methylpseudouridine within RNA duplexes

Physical chemistry chemical physics : PCCP, 2024-01, Vol.26 (2), p.992-999

2024

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Predicting nearest neighbor free energies of modified RNA with LIE: results for pseudouridine and 1-methylpseudouridine within RNA duplexes

Physical chemistry chemical physics : PCCP, 2024-01, Vol.26 (2), p.992-999

2024

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Predicting nearest neighbor free energies of modified RNA with LIE: results for pseudouridine and N 1-methylpseudouridine within RNA duplexes

Physical chemistry chemical physics : PCCP, 2024-01, Vol.26 (2), p.992-999

2024

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Conformations of Flanking Bases in HIV-1 RNA DIS Kissing Complexes Studied by Molecular Dynamics

Biophysical journal, 2007-12, Vol.93 (11), p.3932-3949

2007

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Molecular Dynamics Simulation of the Conformational Preferences of Pseudouridine Derivatives: Improving the Distribution in the Glycosidic Torsion Space

Journal of chemical information and modeling, 2020-10, Vol.60 (10), p.4995-5002

2020

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Inosine and its methyl derivatives: Occurrence, biogenesis, and function in RNA

Progress in biophysics and molecular biology, 2022-03, Vol.169-170, p.21-52

2022

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LNA-induced dynamic stability in a therapeutic aptamer: insights from molecular dynamics simulations

Journal of biomolecular structure & dynamics, 2023-04, Vol.41 (6), p.2221-2230

2023

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The origin of the high stability of 3'-terminal uridine tetrads: contributions of hydrogen bonding, stacking interactions, and steric factors evaluated using modified oligonucleotide analogs

RNA (Cambridge), 2020-12, Vol.26 (12), p.2000-2016

2020

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Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields

Journal of chemical theory and computation, 2009-09, Vol.5 (9), p.2514-2530

2009

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Unraveling the structural basis for the exceptional stability of RNA G-quadruplexes capped by a uridine tetrad at the 3' terminus

RNA (Cambridge), 2019-01, Vol.25 (1), p.121-134

2019

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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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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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Ensemble Allosteric Model for the Modified Wobble Hypothesis

The journal of physical chemistry letters, 2020-08, Vol.11 (15), p.6337-6343

2020

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The oligonucleotides containing N7-regioisomer of guanosine. Influence on thermodynamic properties and structure of RNA duplexes

RNA (Cambridge), 2024-10, p.rna.080106.124

2024

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

Data-informed reparameterization of modified RNA and the effect of explicit water models: application to pseudouridine and derivatives

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

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

Mutations in human AID differentially affect its ability to deaminate cytidine and 5-methylcytidine in ssDNA substrates in vitro

Structural Stability of the Anticodon Stem Loop Domains of the Unmodified Yeast and Escherichia coli tRNAPhe: Differing Views from Different Force Fields

RNA tertiary structure prediction using RNAComposer in CASP15

How bioinformatics resources work with G4 RNAs

Computational and NMR studies of RNA duplexes with an internal pseudouridine-adenosine base pair

Predicting nearest neighbor free energies of modified RNA with LIE: results for pseudouridine and N1-methylpseudouridine within RNA duplexes

Predicting nearest neighbor free energies of modified RNA with LIE: results for pseudouridine and 1-methylpseudouridine within RNA duplexes

Predicting nearest neighbor free energies of modified RNA with LIE: results for pseudouridine and N 1-methylpseudouridine within RNA duplexes

Conformations of Flanking Bases in HIV-1 RNA DIS Kissing Complexes Studied by Molecular Dynamics

Molecular Dynamics Simulation of the Conformational Preferences of Pseudouridine Derivatives: Improving the Distribution in the Glycosidic Torsion Space

Inosine and its methyl derivatives: Occurrence, biogenesis, and function in RNA

LNA-induced dynamic stability in a therapeutic aptamer: insights from molecular dynamics simulations

The origin of the high stability of 3'-terminal uridine tetrads: contributions of hydrogen bonding, stacking interactions, and steric factors evaluated using modified oligonucleotide analogs

Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields

Unraveling the structural basis for the exceptional stability of RNA G-quadruplexes capped by a uridine tetrad at the 3' terminus

Topology-based classification of tetrads and quadruplex structures

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

Ensemble Allosteric Model for the Modified Wobble Hypothesis

The oligonucleotides containing N7-regioisomer of guanosine. Influence on thermodynamic properties and structure of RNA duplexes

Entanglements of structure elements revealed in RNA 3D models

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

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