MODOMICS: a database of RNA modifications and related information. 2023 update

Area of Science:

• Biochemistry
• Bioinformatics
• Molecular Biology

Background:

• The MODOMICS database is a key resource for RNA modification data.
• Previous versions lacked comprehensive coverage of novel RNA modifications and integrated structural data.
• Accurate representation of RNA sequences and their modifications is crucial for understanding biological function.

Purpose of the Study:

• To update and expand the MODOMICS database with recent RNA modification data.
• To enhance the representation of RNA sequences and their modifications.
• To improve data annotation and reliability within the database.

Main Methods:

• Incorporated new data types related to RNA modifications.
• Expanded the modification catalog to include natural and synthetic residues.
• Updated RNA sequence sections with new sequences and alignments for tRNAs and rRNAs.
• Integrated protein structures from RCSB PDB and AlphaFold predictions.
• Implemented a data annotation system with 'Evidence' and 'Estimated Reliability' features.

Main Results:

• MODOMICS now includes an expanded catalog of RNA modifications.
• Enhanced representation of RNA sequences from RCSB PDB.
• Updated protein section linked to structural data and predictions.
• New annotation system provides clarity on data support and accuracy for all entries.

Conclusions:

• The updated MODOMICS database offers a more comprehensive resource for RNA modification research.
• Enhanced data integration and annotation improve the accuracy and utility of RNA modification information.
• The database facilitates better understanding of RNA structure-function relationships.