MODOMICS: a database of RNA modification pathways. 2021 update.

Autor:	Boccaletto P; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland., Stefaniak F; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland., Ray A; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland., Cappannini A; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland., Mukherjee S; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland., Purta E; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland., Kurkowska M; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland., Shirvanizadeh N; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland., Destefanis E; Department of Cellular, Computational and Integrative Biology, University of Trento, Via Sommarive 9, 38123 Trento, Italy., Groza P; Department of Molecular Biology, Umeå University, SE-901 85 Umeå, Sweden.; Wallenberg Centre for Molecular Medicine, Umeå University, SE-901 85 Umeå, Sweden., Avşar G; Department of Bioengineering, Gebze Technical University, 41400 Kocaeli, Turkey., Romitelli A; Core Research Laboratory, ISPRO-Institute for Cancer Research, Prevention and Clinical Network, 50139 Firenze, Italy.; Department of Medical Biotechnologies, Università di Siena., Pir P; Department of Bioengineering, Gebze Technical University, 41400 Kocaeli, Turkey., Dassi E; Department of Cellular, Computational and Integrative Biology, University of Trento, Via Sommarive 9, 38123 Trento, Italy., Conticello SG; Core Research Laboratory, ISPRO-Institute for Cancer Research, Prevention and Clinical Network, 50139 Firenze, Italy.; Institute of Clinical Physiology, National Research Council, 56124 Pisa, Italy., Aguilo F; Department of Molecular Biology, Umeå University, SE-901 85 Umeå, Sweden.; Wallenberg Centre for Molecular Medicine, Umeå University, SE-901 85 Umeå, Sweden., Bujnicki JM; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland.
Jazyk:	angličtina
Zdroj:	Nucleic acids research [Nucleic Acids Res] 2022 Jan 07; Vol. 50 (D1), pp. D231-D235.
DOI:	10.1093/nar/gkab1083
Abstrakt:	The MODOMICS database has been, since 2006, a manually curated and centralized resource, storing and distributing comprehensive information about modified ribonucleosides. Originally, it only contained data on the chemical structures of modified ribonucleosides, their biosynthetic pathways, the location of modified residues in RNA sequences, and RNA-modifying enzymes. Over the years, prompted by the accumulation of new knowledge and new types of data, it has been updated with new information and functionalities. In this new release, we have created a catalog of RNA modifications linked to human diseases, e.g., due to mutations in genes encoding modification enzymes. MODOMICS has been linked extensively to RCSB Protein Data Bank, and sequences of experimentally determined RNA structures with modified residues have been added. This expansion was accompanied by including nucleotide 5'-monophosphate residues. We redesigned the web interface and upgraded the database backend. In addition, a search engine for chemically similar modified residues has been included that can be queried by SMILES codes or by drawing chemical molecules. Finally, previously available datasets of modified residues, biosynthetic pathways, and RNA-modifying enzymes have been updated. Overall, we provide users with a new, enhanced, and restyled tool for research on RNA modification. MODOMICS is available at https://iimcb.genesilico.pl/modomics/. (© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.)
Databáze:	MEDLINE
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