CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures
Figure 1
Comparison of the p1 tunnel of DhaA calculated by CAVER 3.0 and MOLE 1.2.
(A) Time evolution of the bottleneck radius calculated by CAVER 3.0 (blue) and MOLE 1.2 (red). Only a part of the 10 ns MD simulation is shown for clarity. The sample snapshot (black arrows) was taken at 0.81 ns. (B) Geometry of the p1 tunnel in the sample snapshot calculated by CAVER 3.0 (blue) and MOLE 1.2 (red). Hydrogen atom of the bottleneck residue Ala145 (white ball) is shown together with the sulfur atom of the bottleneck residue Cys176 (yellow ball) and with sphere representation of the tunnels. The underestimation of the bottleneck radius by MOLE 1.2 is visible as an empty space between the tunnel and the hydrogen atom of Ala145. (C) Profile of the p1 tunnel in the sample snapshot calculated by CAVER 3.0 (blue) and MOLE 1.2 (red). The dashed line indicates the profile representing the maximum possible difference between the CAVER-calculated (solid line) and the correct profile of the p1 tunnel.