Figure 7
From: CAVER: a new tool to explore routes from protein clefts, pockets and cavities
Tunnels' gorges as found by CAVER in MD trajectories. Analysis of snapshots taken from a molecular dynamics simulation of DhlA (A), DhaA (B) and LinB (C). Two clusters of tunnel gorges were identified in DhlA simulation (denoted by the numbers 1 and 2). Three clusters were identified in the DhaA simulation (denoted by the numbers 1–3) and one cluster was identified in the LinB simulation. Tunnel gorges are represented by small balls. Ball color correlates with gorge radius, balls representing narrow gorges are red and wide gorges are blue. The mesh represents the protein surface.