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

Andrea Cappannini(International Institute of Molecular and Cell Biology), Angana Ray(International Institute of Molecular and Cell Biology), Elżbieta Purta(International Institute of Molecular and Cell Biology), Sunandan Mukherjee(International Institute of Molecular and Cell Biology), Pietro Boccaletto(International Institute of Molecular and Cell Biology), S Naeim Moafinejad(International Institute of Molecular and Cell Biology), Antony Lechner(Centre National de la Recherche Scientifique), Charles Barchet(Centre National de la Recherche Scientifique), Bruno P. Klaholz(Centre National de la Recherche Scientifique), Filip Stefaniak(International Institute of Molecular and Cell Biology), Janusz M. Bujnicki(International Institute of Molecular and Cell Biology)
Nucleic Acids Research
November 28, 2023
10.1093/nar/gkad1083
Cited by 389Open Access
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Abstract

The MODOMICS database was updated with recent data and now includes new data types related to RNA modifications. Changes to the database include an expanded modification catalog, encompassing both natural and synthetic residues identified in RNA structures. This addition aids in representing RNA sequences from the RCSB PDB database more effectively. To manage the increased number of modifications, adjustments to the nomenclature system were made. Updates in the RNA sequences section include the addition of new sequences and the reintroduction of sequence alignments for tRNAs and rRNAs. The protein section was updated and connected to structures from the RCSB PDB database and predictions by AlphaFold. MODOMICS now includes a data annotation system, with 'Evidence' and 'Estimated Reliability' features, offering clarity on data support and accuracy. This system is open to all MODOMICS entries, enhancing the accuracy of RNA modification data representation. MODOMICS is available at https://iimcb.genesilico.pl/modomics/.

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