Czerwoniec Anna, Dunin-Horkawicz Stanislaw, Purta Elzbieta, Kaminska Katarzyna H, Kasprzak Joanna M, Bujnicki Janusz M, Grosjean Henri, Rother Kristian
Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland.
Nucleic Acids Res. 2009 Jan;37(Database issue):D118-21. doi: 10.1093/nar/gkn710. Epub 2008 Oct 14.
MODOMICS, a database devoted to the systems biology of RNA modification, has been subjected to substantial improvements. It provides comprehensive information on the chemical structure of modified nucleosides, pathways of their biosynthesis, sequences of RNAs containing these modifications and RNA-modifying enzymes. MODOMICS also provides cross-references to other databases and to literature. In addition to the previously available manually curated tRNA sequences from a few model organisms, we have now included additional tRNAs and rRNAs, and all RNAs with 3D structures in the Nucleic Acid Database, in which modified nucleosides are present. In total, 3460 modified bases in RNA sequences of different organisms have been annotated. New RNA-modifying enzymes have been also added. The current collection of enzymes includes mainly proteins for the model organisms Escherichia coli and Saccharomyces cerevisiae, and is currently being expanded to include proteins from other organisms, in particular Archaea and Homo sapiens. For enzymes with known structures, links are provided to the corresponding Protein Data Bank entries, while for many others homology models have been created. Many new options for database searching and querying have been included. MODOMICS can be accessed at http://genesilico.pl/modomics.
MODOMICS是一个致力于RNA修饰系统生物学的数据库，已经有了实质性的改进。它提供了关于修饰核苷化学结构、生物合成途径、含有这些修饰的RNA序列以及RNA修饰酶的全面信息。MODOMICS还提供了与其他数据库和文献的交叉引用。除了之前从少数模式生物中手动整理的tRNA序列外，我们现在还纳入了更多的tRNA和rRNA，以及核酸数据库中所有具有三维结构且存在修饰核苷的RNA。总共注释了不同生物体RNA序列中的3460个修饰碱基。还添加了新的RNA修饰酶。目前的酶集合主要包括来自模式生物大肠杆菌和酿酒酵母的蛋白质，并且目前正在扩展以纳入来自其他生物体的蛋白质，特别是古细菌和智人的蛋白质。对于具有已知结构的酶，提供了与相应蛋白质数据库条目的链接，而对于许多其他酶则创建了同源模型。还纳入了许多新的数据库搜索和查询选项。可通过http://genesilico.pl/modomics访问MODOMICS。
