The InterRNA database was built using MySQL version 5.1.44 and PHP version 5.3.15

consists of nucleic acid base interactions in PDB formatted RNA structures that were selected based on X-ray method with resolutions higher than 4.0 Angstroms and containing RNA chains. These structures were then been annotated using the computer programs NASSAM and COGNAC.

There are two dataset used in this database which are manual curated dataset and automated annotation dataset. The manual curated dataset consists of 64 RNA structures is adapted from the work of Xin et al. 2008 plus several new riboswitch and ribozyme structures. The automated dataset consist of 2158 RNA structures that were downloaded from the PDB website on 3/9/2014.

• Datasets generated by NASSAM annotations
  The NASSAM program searches for five types of known motifs which are A-minor, base triple, tetraloop, ribose-zipper and T-loop motifs. The searches are based on distances between the bases that are represented as pseudoatom vectors.
  
  
• Automated NASSAM annotations
  The available RNA structures in the PDB were annotated and 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.
  
  
• Manually Curated NASSAM Annotations
  A high-resolution subset of RNA structures (higher than 3.05 Angstroms) were also manually curated where each motif identified by NASSAM was visually examined and verified to conform to the search pattern.
  
  
• Datasets generated by COGNAC annotations
  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.
  
  

1. The download option to download the search results in CSV format


2. The motif visualization using JSmol


3. The hydrogen bonding interaction data involved in the motif of network

The database is updated on a monthly basis.

If you have any comments, queries or to report errors, please contact us at