Programs for representing the surface of a channel inside protein

From CCP4 wiki

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

  1. PASS
  2. Pymol with Caver scripts: http://www.pymol.org and http://loschmidt.chemi.muni.cz/caver/download.php
  3. HOLE. http://d2o.biop.ox.ac.uk:38080/
  4. CASTp. http://sts-fw.bioengr.uic.edu/castp/ or http://www.cgl.ucsf.ed/chimera
  5. MOLE. http://troll.chemi.muni.cz/whitezone/development/mole/online/moleonline1.3/ or http://mole.chemi.muni.cz/download.php
  6. HOLLOW. http://hollow.sourceforge.net/.
  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) http://pubs.acs.org/cgi-bin/abstract.cgi/bichaw/2008/47/i11/abs/bi702386t.html