Topology-based classification of tetrads and quadruplex structures
| Autor: | Tomasz Zok, Joanna Sarzynska, Joanna Miskiewicz, Mariusz Popenda, Marta Szachniuk |
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| Rok vydání: | 2019 |
| Předmět: |
Statistics and Probability
0303 health sciences Computer science computer.file_format 010402 general chemistry Topology Protein Data Bank Original Papers Structural Bioinformatics 01 natural sciences Biochemistry Protein Structure Secondary 0104 chemical sciences Computer Science Applications G-Quadruplexes 03 medical and health sciences Computational Mathematics Computational Theory and Mathematics Nucleic acid Molecular Biology Protein secondary structure computer 030304 developmental biology |
| Zdroj: | Bioinformatics |
| ISSN: | 1367-4811 1367-4803 |
| Popis: | Motivation Quadruplexes 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. Results In 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. |
| Databáze: | OpenAIRE |
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