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. 2014 May 15;42(Web Server issue):W382–W388. doi: 10.1093/nar/gku438

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© The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 3. — Examples of COGNAC output: (A) the molecular visualization interface using JSmol (or Jmol) with basic information on the structure, external links to the PDB entry and a listing of the hydrogen bonds involved in the interaction network which in this case is a base quadruple; (B) two matches for a type II quadruple (refer to Figure 2B) search tree query in a lysine riboswitch structure—a GGGG quadruple (center panel, in green) and a CUCU quadruple (center panel, in blue) that upon further scrutiny is interconnected (denoted by red line) to form an octuple base interaction (center panel).