MODOMICS is an extensive database dedicated to the systems biology of RNA modification, providing comprehensive information on chemical structures of modified nucleosides, biosynthesis pathways, RNA sequences with these modifications, and RNA-modifying enzymes. The database has been significantly enhanced with new data, including additional tRNAs, rRNAs, and 3D structures of modified nucleosides. It now includes over 3460 annotated modified bases in RNA sequences from various organisms. New RNA-modifying enzymes have been added, primarily from model organisms like *Escherichia coli* and *Saccharomyces cerevisiae*, with ongoing expansion to include proteins from other organisms. The database also offers links to Protein Data Bank entries for enzymes with known structures and homology models for those without experimental structures. MODOMICS provides various options for searching and querying, and can be accessed at http://genesilico.pl/modomics. The database aims to facilitate research on RNA modification pathways and is part of a broader network of RNA systems biology resources.MODOMICS is an extensive database dedicated to the systems biology of RNA modification, providing comprehensive information on chemical structures of modified nucleosides, biosynthesis pathways, RNA sequences with these modifications, and RNA-modifying enzymes. The database has been significantly enhanced with new data, including additional tRNAs, rRNAs, and 3D structures of modified nucleosides. It now includes over 3460 annotated modified bases in RNA sequences from various organisms. New RNA-modifying enzymes have been added, primarily from model organisms like *Escherichia coli* and *Saccharomyces cerevisiae*, with ongoing expansion to include proteins from other organisms. The database also offers links to Protein Data Bank entries for enzymes with known structures and homology models for those without experimental structures. MODOMICS provides various options for searching and querying, and can be accessed at http://genesilico.pl/modomics. The database aims to facilitate research on RNA modification pathways and is part of a broader network of RNA systems biology resources.