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ASC-G4, an algorithm to calculate advanced structural characteristics of G-quadruplexes

ASC-G4 is an algorithm for the calculation of the advanced structural characteristics of G-quadruplexes (G4). It allows the unambiguous determination of the intramolecular G4 topology, based on the oriented strand numbering. It also resolves the ambiguity in the determination of the guanine glycosid...

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Autores principales: Farag, Marc, Messaoudi, Cédric, Mouawad, Liliane
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10018348/
https://www.ncbi.nlm.nih.gov/pubmed/36794725
http://dx.doi.org/10.1093/nar/gkad060
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author Farag, Marc
Messaoudi, Cédric
Mouawad, Liliane
author_facet Farag, Marc
Messaoudi, Cédric
Mouawad, Liliane
author_sort Farag, Marc
collection PubMed
description ASC-G4 is an algorithm for the calculation of the advanced structural characteristics of G-quadruplexes (G4). It allows the unambiguous determination of the intramolecular G4 topology, based on the oriented strand numbering. It also resolves the ambiguity in the determination of the guanine glycosidic configuration. With this algorithm, we showed that the use of the C3’ or C5’ atoms to calculate the groove width in G4 is more appropriate than the P atoms and that the groove width does not always reflect the space available within the groove. For the latter, the minimum groove width is more appropriate. The application of ASC-G4 to 207 G4 structures guided the choices made for the calculations. A website based on ASC-G4 (http://tiny.cc/ASC-G4) was created, where the user uploads his G4 structure and gets its topology, the types of its loops and their lengths, the presence of snapbacks and bulges, the distribution of guanines in the tetrads and strands, the glycosidic configuration of these guanines, their rise, the groove widths, the minimum groove widths, the tilt and twist angles, the backbone dihedral angles, etc. It also provides a large number of atom-atom and atom-plane distances that are relevant to evaluating the quality of the structure.
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spelling pubmed-100183482023-03-17 ASC-G4, an algorithm to calculate advanced structural characteristics of G-quadruplexes Farag, Marc Messaoudi, Cédric Mouawad, Liliane Nucleic Acids Res Computational Biology ASC-G4 is an algorithm for the calculation of the advanced structural characteristics of G-quadruplexes (G4). It allows the unambiguous determination of the intramolecular G4 topology, based on the oriented strand numbering. It also resolves the ambiguity in the determination of the guanine glycosidic configuration. With this algorithm, we showed that the use of the C3’ or C5’ atoms to calculate the groove width in G4 is more appropriate than the P atoms and that the groove width does not always reflect the space available within the groove. For the latter, the minimum groove width is more appropriate. The application of ASC-G4 to 207 G4 structures guided the choices made for the calculations. A website based on ASC-G4 (http://tiny.cc/ASC-G4) was created, where the user uploads his G4 structure and gets its topology, the types of its loops and their lengths, the presence of snapbacks and bulges, the distribution of guanines in the tetrads and strands, the glycosidic configuration of these guanines, their rise, the groove widths, the minimum groove widths, the tilt and twist angles, the backbone dihedral angles, etc. It also provides a large number of atom-atom and atom-plane distances that are relevant to evaluating the quality of the structure. Oxford University Press 2023-02-16 /pmc/articles/PMC10018348/ /pubmed/36794725 http://dx.doi.org/10.1093/nar/gkad060 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Computational Biology
Farag, Marc
Messaoudi, Cédric
Mouawad, Liliane
ASC-G4, an algorithm to calculate advanced structural characteristics of G-quadruplexes
title ASC-G4, an algorithm to calculate advanced structural characteristics of G-quadruplexes
title_full ASC-G4, an algorithm to calculate advanced structural characteristics of G-quadruplexes
title_fullStr ASC-G4, an algorithm to calculate advanced structural characteristics of G-quadruplexes
title_full_unstemmed ASC-G4, an algorithm to calculate advanced structural characteristics of G-quadruplexes
title_short ASC-G4, an algorithm to calculate advanced structural characteristics of G-quadruplexes
title_sort asc-g4, an algorithm to calculate advanced structural characteristics of g-quadruplexes
topic Computational Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10018348/
https://www.ncbi.nlm.nih.gov/pubmed/36794725
http://dx.doi.org/10.1093/nar/gkad060
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