Citation for referencing COGNAC:
1. Mohd Firdaus-Raih, Hazrina Yusof Hamdani, Nurul Nadzirin, Effirul Ikhwan Ramlan, Peter Willett and Peter J. Artymiuk. 2014. COGNAC: a web server for searching and annotating hydrogen-bonded base interactions in RNA three-dimensional structures. Nucleic Acids Res. 42 (W1): W382-W388. HTML, PDF
To run a search:
STEP 1. Select to search either the option of (1) searching for a specific set of hydrogen bonded base connections in a database of RNA structures (sourced from the PDB) or (2) to upload an RNA structure (in PDB format) to annotate the hydrogen bonded base interactions present in the query structure.
Select the number of residues and the arrangement of the interactions for the query patterns from the list provided (2-6 bases or select "All patterns" for arrangement types).
STEP 3. For specific patterns selected in STEP 2; enter the specific residue or general type (for all base possibilities).
For searches using Option 3; the difference is mainly in the requirement to have two structures uploaded. Please note that the program does not filter out highly dissimilar structures which are not useful comparisons.
Search times and output visualization:
1. Each search may take time to complete depending on the complexity of the query and the server load (usually completed within 2 minutes). Users are advised to bookmark the results page or copy the link to the results for analysis at a later point in time if a search takes more than 10 minutes.
2. Please note that COGNAC output can be visualized using JSMol. This bypasses issues with Java such as the block by the Mac OSX operating system when using Jmol.
3. Search results will be kept for at least 2 days. The main search results can be downloaded to your local computer while still retaining the server side ability to view the hits in Jmol.
Please email firstname.lastname@example.org for help or if you've detected any problems with the search.