COGNAC

COGNAC identifies and annotates hydrogen-bonded base interactions in three-dimensional RNA structures to characterize networks of hydrogen bonds and potential tertiary motifs.

Key Features:

• Identification of Hydrogen-Bond Networks: Detects unbroken networks of hydrogen-bonded base interactions within 3D RNA structures.
• Graph-Theoretical Analysis: Applies a graph-theoretical algorithm to represent hydrogen bonds as interaction networks and analyze their topology at atomic resolution.
• Comparative Analysis: Compares hydrogen-bond networks between different RNA structures to map atomic-level differences arising from conformational changes, mutations, or binding events.
• Potential Tertiary Motif Identification: Recognizes clusters of hydrogen bonds as potential tertiary motifs relevant to RNA stability and function.
• Annotation and Search of Interactions: Searches for and annotates hydrogen-bonded base interactions within three-dimensional RNA structures.

Scientific Applications:

• RNA Structure–Function Analysis: Provides annotated hydrogen-bond networks to inform studies of how structural features influence RNA stability and function.
• Mapping Effects of Mutations and Binding: Identifies atomic-level differences in hydrogen-bonding that result from genetic mutations or protein–RNA binding events.
• Tertiary Motif Characterization: Aids identification of hydrogen-bond clusters as candidate tertiary motifs for understanding RNA structural and functional aspects.

Methodology:

Translates 3D RNA structures into graphs of hydrogen-bonded base interactions and applies graph-theoretical algorithms to identify unbroken networks and compare networks between structures.