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GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies

Fig 1

Graph representation of the xpt-pbuX guanine riboswitch aptamer domain (PDB ID: 4FE5).

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.

Fig 1