MODOMICS is a database focused on RNA modification pathways, providing comprehensive information on modified nucleosides, their biosynthesis pathways, RNA sequences with modifications, and RNA-modifying enzymes. The database has been updated with new data, including additional tRNA and rRNA sequences, and all RNAs with 3D structures in the Nucleic Acid Database. Over 3460 modified bases in RNA sequences from different organisms have been annotated. New RNA-modifying enzymes have also been added, with a focus on model organisms like Escherichia coli and Saccharomyces cerevisiae, and expansion to include proteins from Archaea and Homo sapiens. For enzymes with known structures, links to the Protein Data Bank are provided, while homology models are created for others. The database includes new search and query options, and can be accessed at http://genesilico.pl/modomics. The database contains 119 different RNA modifications, with detailed information on each, including chemical properties, phylogenetic distribution, and RNA types. Modifications are categorized by name, origin, and chemical groups. Chemical structures are represented by SMILE codes, 2D plots, and 3D structures. Reactions involving modified nucleosides are annotated separately. Pathways can be viewed in their entirety or zoomed in on specific subpathways. MODOMICS contains information on over 100 RNA-modifying enzymes and co-factors. Enzymes are categorized by organism and reaction type, with details on their function and structure. Enzymes with known structures are linked to the Protein Data Bank, while homology models are provided for others. Enzyme names follow a new nomenclature system, with a three-part naming convention. MODOMICS provides RNA sequences with modifications, including multiple sequence alignments for homologous RNAs. It includes tRNA and rRNA sequences from various sources, with modifications curated manually. Sequences are visualized with modifications highlighted and secondary structures indicated. The database also provides structure files, images, and program code for parsing data. A new nomenclature system for RNA modifications and enzymes has been proposed to address formatting issues in machine-centric data formats. The system uses numerical prefixes to uniquely identify modifications and enzymes. The database is freely accessible for research and provides data in plain text formats, structure files, and images. It is part of a broader RNA systems biology network and integrates with general pathway resources like KEGG and enzyme databases like BRENDA. Funding was provided by the Polish Ministry of Science and Higher Education and the EU.MODOMICS is a database focused on RNA modification pathways, providing comprehensive information on modified nucleosides, their biosynthesis pathways, RNA sequences with modifications, and RNA-modifying enzymes. The database has been updated with new data, including additional tRNA and rRNA sequences, and all RNAs with 3D structures in the Nucleic Acid Database. Over 3460 modified bases in RNA sequences from different organisms have been annotated. New RNA-modifying enzymes have also been added, with a focus on model organisms like Escherichia coli and Saccharomyces cerevisiae, and expansion to include proteins from Archaea and Homo sapiens. For enzymes with known structures, links to the Protein Data Bank are provided, while homology models are created for others. The database includes new search and query options, and can be accessed at http://genesilico.pl/modomics. The database contains 119 different RNA modifications, with detailed information on each, including chemical properties, phylogenetic distribution, and RNA types. Modifications are categorized by name, origin, and chemical groups. Chemical structures are represented by SMILE codes, 2D plots, and 3D structures. Reactions involving modified nucleosides are annotated separately. Pathways can be viewed in their entirety or zoomed in on specific subpathways. MODOMICS contains information on over 100 RNA-modifying enzymes and co-factors. Enzymes are categorized by organism and reaction type, with details on their function and structure. Enzymes with known structures are linked to the Protein Data Bank, while homology models are provided for others. Enzyme names follow a new nomenclature system, with a three-part naming convention. MODOMICS provides RNA sequences with modifications, including multiple sequence alignments for homologous RNAs. It includes tRNA and rRNA sequences from various sources, with modifications curated manually. Sequences are visualized with modifications highlighted and secondary structures indicated. The database also provides structure files, images, and program code for parsing data. A new nomenclature system for RNA modifications and enzymes has been proposed to address formatting issues in machine-centric data formats. The system uses numerical prefixes to uniquely identify modifications and enzymes. The database is freely accessible for research and provides data in plain text formats, structure files, and images. It is part of a broader RNA systems biology network and integrates with general pathway resources like KEGG and enzyme databases like BRENDA. Funding was provided by the Polish Ministry of Science and Higher Education and the EU.