GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies
Nodes (players) are built from the secondary structure representation in which base-paired nucleotides are shown in blue and free nucleotides are shown in yellow. Blue nodes correspond to helices and yellow nodes to junctions. Each element, except the three-way junction is represented by one node (shown as a sphere), taken to be the geometric center of the heavy atoms. The three-way junction contains two nodes, accounting for helical stacking and branching, respectively.