ArticleBioinformatics (Oxford, England)2020
Topology-based classification of tetrads and quadruplex structures.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Non-Random Distribution of G-Quadruplex Structures Reveals Regulatory and Ecological Adaptations in Bacterial Genomes.International journal of molecular sciences · 2025Article
- G4STAB: a multi-input deep learning model to predict G-quadruplex thermodynamic stability based on sequence and salt concentration.Bioinformatics (Oxford, England) · 2025Article
- Detecting polynucleotide motifs: Pentads, hexads, and beyond.PLoS computational biology · 2025Article
- Exploring the G-Quadruplex Formation of AS1411 Derivatives.Molecules (Basel, Switzerland) · 2025Article
- Kanamycin and G-Quadruplexes: An Exploration of Binding Interactions.Molecules (Basel, Switzerland) · 2024Article
- Comprehensive analysis of intramolecular G-quadruplex structures: furthering the understanding of their formalism.Nucleic acids research · 2024Article
- WebTetrado: a webserver to explore quadruplexes in nucleic acid 3D structures.Nucleic acids research · 2023Article
- ASC-G4, an algorithm to calculate advanced structural characteristics of G-quadruplexes.Nucleic acids research · 2023Article
- The first crystal structures of hybrid and parallel four-tetrad intramolecular G-quadruplexes.Nucleic acids research · 2022Article
- Contact networks in RNA: a structural bioinformatics study with a new tool.Journal of computer-aided molecular design · 2022Article
- ONQUADRO: a database of experimentally determined quadruplex structures.Nucleic acids research · 2022Article
- Ligands as Stabilizers of G-Quadruplexes in Non-Coding RNAs.Molecules (Basel, Switzerland) · 2021Review
- How bioinformatics resources work with G4 RNAs.Briefings in bioinformatics · 2021Review
- 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 (New York, N.Y.) · 2020Article
- DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL.Nucleic acids research · 2020Article
- ElTetrado: a tool for identification and classification of tetrads and quadruplexes.BMC bioinformatics · 2020Article
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
motivationQuadruplexes attract the attention of researchers from many fields of bio-science. Due to a specific structure, these tertiary motifs are involved in various biological processes. They are also promising therapeutic targets in many strategies of drug development, including anticancer and neurological disease treatment. The uniqueness and diversity of their forms cause that quadruplexes show great potential in novel biological applications. The existing approaches for quadruplex analysis are based on sequence or 3D structure features and address canonical motifs only.
resultsIn our study, we analyzed tetrads and quadruplexes contained in nucleic acid molecules deposited in Protein Data Bank. Focusing on their secondary structure topology, we adjusted its graphical diagram and proposed new dot-bracket and arc representations. We defined the novel classification of these motifs. It can handle both canonical and non-canonical cases. Based on this new taxonomy, we implemented a method that automatically recognizes the types of tetrads and quadruplexes occurring as unimolecular structures. Finally, we conducted a statistical analysis of these motifs found in experimentally determined nucleic acid structures in relation to the new classification. AVAILABILITY AND IMPLEMENTATION: https://github.com/tzok/eltetrado/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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