Evidence map›Paper›PMID 38835951›Full record

ArticleNAR genomics and bioinformatics2024

From RNA sequence to its three-dimensional structure: geometrical structure, stability and dynamics of selected fragments of SARS-CoV-2 RNA.

Leonid Gorb, Ivan Voiteshenko, Vasyl Hurmach, Margarita Zarudnaya, Alex Nyporko, Tetiana Shyryna, Maksym Platonov, Szczepan Roszak, Bakhtiyor Rasulev

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in NAR genomics and bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Leonid GorbDepartment of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv 03143, Ukraine.ORCID https://orcid.org/0000-0001-7932-9105
Ivan VoiteshenkoDepartment of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv 03143, Ukraine.ORCID https://orcid.org/0000-0003-2434-9218
Vasyl HurmachDepartment of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv 03143, Ukraine.ORCID https://orcid.org/0000-0002-0844-1586
Margarita ZarudnayaDepartment of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv 03143, Ukraine.ORCID https://orcid.org/0000-0002-9601-3126
Alex NyporkoTaras Shevchenko National University of Kyiv, 60 Volodymyrska Street, Kyiv01033, Ukraine.ORCID https://orcid.org/0000-0003-1664-6837
Tetiana ShyrynaDepartment of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv 03143, Ukraine.ORCID https://orcid.org/0000-0003-3278-8384
Maksym PlatonovDepartment of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv 03143, Ukraine.ORCID https://orcid.org/0000-0002-3205-3305
Szczepan RoszakFaculty of Chemistry, University of Wrocław, 50-370Wrocław, Poland.ORCID https://orcid.org/0000-0002-3569-2321
Bakhtiyor RasulevDepartment of Coatings and Polymer Materials, North Dakota State University, NDSU Department 2760, PO Box 6050, Fargo, ND 58108, USA.ORCID https://orcid.org/0000-0002-7845-4884

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

In this computational study, we explore the folding of a particular sequence using various computational tools to produce two-dimensional structures, which are then transformed into three-dimensional structures. We then study the geometry, energetics and dynamics of these structures using full electron quantum-chemical and classical molecular dynamics calculations. Our study focuses on the SARS-CoV-2 RNA fragment GGaGGaGGuguugcaGG and its various structures, including a G-quadruplex and five different hairpins. We examine the impact of two types of counterions (K

Identifiers

PMID38835951
PMCPMC11148665

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.