The InterRNA database consists of base interactions in RNA structures that were annotated using the computer programs NASSAM and COGNAC.
Using the computer program NASSAM, we have annotated available RNA structures in the PDB. To achieve this, the search graphs for 3D motifs that have been reported in the literature were handcrafted as queries using very strict tolerances that we have previously shown to be capable of accurately identifying these motifs. A high resolution subset of RNA structures were also manually curated with the assistance of the NASSAM program where each motif identified was visually examined and validated.
Because there are clear limitations with annotating interactions that have been identified as motifs in the literature, we have taken into consideration that bases that are involved in multiple hydrogen bonds are likely to be stable, and this increased stability may be of structural and indirectly, functional relevance. In order to carry out such an annotation, the hydrogen bonds for all available RNA structures in the dataset were generated. This hydrogen bonding data was then annotated for occurrences where bases were interconnected by the occurrences of hydrogen bonds using our previously reported program COGNAC. At present, the coverage of the database includes very large interconnected base networks that number up to six base residues.
The data entries are searchable via the main search interface or the user can opt to browse through the available entries. Each entry is provided a JSmol interface and the hydrogen bonding interaction data involved in the motif of network.