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

Pietro Boccaletto1, Filip Stefaniak1, Angana Ray1

  • 1Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland.

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|December 11, 2021
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Summary
This summary is machine-generated.

The MODOMICS database now links RNA modifications to human diseases and includes new search tools for chemical similarity. This enhanced resource provides updated information on modified ribonucleosides, pathways, and enzymes for RNA modification research.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Bioinformatics

Background:

  • The MODOMICS database has served as a central repository for modified ribonucleoside information since 2006.
  • It originally focused on chemical structures, biosynthetic pathways, RNA locations, and modifying enzymes.
  • Continuous updates have been necessary due to accumulating knowledge and new data types.

Purpose of the Study:

  • To present a significantly enhanced version of the MODOMICS database.
  • To expand the database with new functionalities and data types, including links to human diseases.
  • To improve user accessibility and research capabilities in RNA modification.

Main Methods:

  • Curated and integrated data on modified ribonucleosides, including chemical structures, pathways, and enzyme information.
  • Developed a new catalog linking RNA modifications to human diseases.
  • Integrated data with the RCSB Protein Data Bank and added experimentally determined RNA structures.
  • Included nucleotide 5'-monophosphate residues and implemented a chemical similarity search engine (SMILES-based).
  • Redesigned the web interface and upgraded the database backend.

Main Results:

  • The updated MODOMICS database now features a catalog of RNA modifications associated with human diseases.
  • Extensive linking to the RCSB Protein Data Bank and inclusion of RNA structure data with modified residues.
  • Introduction of a novel search engine for chemically similar modified residues.
  • Inclusion of nucleotide 5'-monophosphate residues.
  • Updated datasets for modified residues, biosynthetic pathways, and RNA-modifying enzymes.

Conclusions:

  • The MODOMICS database has been substantially enhanced, offering a restyled and more powerful tool for RNA modification research.
  • The new features, including disease links and chemical similarity search, broaden its utility for scientists.
  • This updated resource facilitates deeper investigation into the roles of RNA modifications in biological processes and diseases.