Programs for representing the surface of a channel inside protein

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The following programs can be used for representing the surface of a channel inside protein.

  1. PASS
  2. Pymol with Caver scripts: and
  3. HOLE.
  4. CASTp. or http://www.cgl.ucsf.ed/chimera
  5. MOLE. or
  6. HOLLOW.
  7. The program O can this with following protocol
    • 1/ make object of solvents in the tunnel, sel_off, sel_prop, sel_vis, sphere centred on tunnel...
    • 2/ mask from these solvents, ncs_mask_sph, ncs_mask_lay
    • 3/ asa of just protein
    • 4/ copy space group info from an electron density map to the asa 'map'
    • 5/ average the asa map, using the mask, and IDENT operator, no expansion gives a new map with a surface just around the tunnel.
  8. use CAVENV to identify the channel and confirm the channel by solving the structure of Xenon-pressured crystals - see "Xenon in and at the End of the Tunnel of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase" (Tzanko I. Doukov, Leah C. Blasiak, Javier Seravalli, Stephen W. Ragsdale, and Catherine L. Drennan)