StructRMDB: A database of RNA modification sites that affect RNA secondary structure

Post-transcriptional RNA modifications, prevalent in multiple RNA species such as mRNA, rRNA, and tRNA, play a significant role in biological processes by altering RNA structures. With recent advancements in prediction algorithms, it is possible to predict RNA secondary structure for sequences containing modified bases. In this study, we introduce StructRMDB, the first database designed to characterize the impact of chemical modifications on RNA secondary structure. StructRMDB comprises more than 880,000 RNA modification sites and their structural impacts, including N ⁶ -Methyladenosine (m⁶A), pseudouridine (Ψ), and adenosine-to-inosine editing (A-to-I) from nine species in both pre-RNA and mature RNA. Two RNA secondary structure prediction tools (RNAstructure and ViennaRNA), along with four scoring methods (Similarity Score, Relative Score, Distance, and SMC Score), were adopted to assess structural changes induced by these modifications. Additionally, we visualized RNA secondary structures with and without modifications to highlight structural alterations. A user-friendly graphical interface is provided to facilitate the querying, downloading, and sharing of modified site evaluation and annotation data, offering novel insights into the effects of RNA modifications on secondary structure. StructRMDB serves as a valuable resource for studying the structural impact of RNA modifications and is available at: http://www.rnamd.org/StructRMDB/index.html.