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Figure 8 | BMC Bioinformatics

Figure 8

From: CHEXVIS: a tool for molecular channel extraction and visualization

Figure 8

Comparison of pores extracted by MOLE, MOLAXIS, POREWALKER and CHEXVIS in 2J1N.(a) Cartoon representation of the transmembrane protein 2J1N. This structure consists of three beta-barrel subunits going across the cell membrane. The figure shows top view of the protein such that cell membrane is parallel to the plane of the page. (b) MOLE identifies two pores in this structure, both of them are not correct transmembrane pore passing through beta-barrels. MOLE wrongly identifies the narrow space between the three units as a transmembrane pore. (c) MOLAXIS also identifies a pore going through space between three subunits. This maybe due to the specified input parameters. (d) POREWALKER also fails to identify the correct transmembrane pores in this structure. It identifies the empty space between three subunits as the only transmembrane pore. By design, POREWALKER would not have been able to identify all the three transmembrane pores as it extracts only one transmembrane pore. (e) CHEXVIS is able to correctly identify transmembrane pores through all the three subunits, using default parameters for finding pores. (f) Unlike other tools which identify pore through the space between subunits, the top transmembrane pore identified by CHEXVIS is one of the pore passing through a beta-barrel subunit.

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