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Fig. 1. Access route to protein active site calculated using CAVER and represented by small magneta balls.
Fig. 2. Access tunnel to protein active site represented by a dotted surface.
Fig. 3. Access tunnel to protein active site represented by magneta balls maximally inscribed in node positions.
Fig. 4. Access tunnel calculated using CAVER (red wire) superimposed with the protein cavity calculated using CAST (blue surface).
Fig. 5. Distribution of tunnel gorges (bottle-necks) as found by CAVER analyzing MD trajectory. Protein is represented by black mesh.
Fig. 6. Path found by CAVER analyzing RNA structure (1c2w).
Fig. 7. Two paths found by CAVER analyzing ferrierite structure (zeolit).
Following video shows visualisation of export routes in program PyMol. Molecule and its trajectory were loaded into PyMol and visualised using PyMol-script files generated by CAVER.
Access tunnel to active site is represented by a white mesh. Seen are changes of tunnel shape in several snapshots of molecular dynamic trajectory. Visible are changes in tunnel direction due to occassional close up of a major export route. . Escape path was not found by CAVER for a few snapshots suggesting short-time inaccessbility of the active site.
