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  • Boccaletto, PietroLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland (author)

MODOMICS: a database of RNA modification pathways. 2021 update

  • Article/chapterEnglish2022

Publisher, publication year, extent ...

  • 2021-12-06
  • Oxford University Press,2022
  • electronicrdacarrier

Numbers

  • LIBRIS-ID:oai:DiVA.org:umu-192884
  • https://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-192884URI
  • https://doi.org/10.1093/nar/gkab1083DOI

Supplementary language notes

  • Language:English
  • Summary in:English

Part of subdatabase

Classification

  • Subject category:ref swepub-contenttype
  • Subject category:art swepub-publicationtype

Notes

  • Issue Section: Database Issue
  • 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/.

Subject headings and genre

Added entries (persons, corporate bodies, meetings, titles ...)

  • Stefaniak, FilipLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland (author)
  • Ray, AnganaLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland (author)
  • Cappannini, AndreaLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland (author)
  • Mukherjee, SunandanLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland (author)
  • Purta, ElżbietaLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland (author)
  • Kurkowska, MałgorzataLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland (author)
  • Shirvanizadeh, NiloofarLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland (author)
  • Destefanis, ElianaDepartment of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy (author)
  • Groza, PaulaUmeå universitet,Wallenberg centrum för molekylär medicin vid Umeå universitet (WCMM),Institutionen för molekylärbiologi (Medicinska fakulteten)(Swepub:umu)pape8310 (author)
  • Avşar, GülbenDepartment of Bioengineering, Gebze Technical University, Kocaeli, Turkey (author)
  • Romitelli, AntoniaCore Research Laboratory, ISPRO-Institute for Cancer Research, Prevention and Clinical Network, Firenze, Italy; Department of Medical Biotechnologies, Università di Siena (author)
  • Pir, PınarDepartment of Bioengineering, Gebze Technical University, Kocaeli, Turkey (author)
  • Dassi, ErikDepartment of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy (author)
  • Conticello, Silvestro G.Core Research Laboratory, ISPRO-Institute for Cancer Research, Prevention and Clinical Network, Firenze, Italy; Institute of Clinical Physiology, National Research Council, Pisa, Italy (author)
  • Aguilo, Francesca,PhDUmeå universitet,Wallenberg centrum för molekylär medicin vid Umeå universitet (WCMM),Institutionen för molekylärbiologi (Medicinska fakulteten)(Swepub:umu)frag0008 (author)
  • Bujnicki, Janusz M.Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland (author)
  • Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, PolandLaboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland (creator_code:org_t)

Related titles

  • In:Nucleic Acids Research: Oxford University Press50:D1, s. D231-D2350305-10481362-4962

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