Channel Finder

Input structure:
Upload PDB file to process:

Enter PDB ID to process:
 

Use biological unit?

Use hetero atoms?

Grid resolution:
crude low medium high

PyMOL compatible
Create Water PDB
Share your results

Outer probe radius:


Inner probe radius:


Choose one of the following options:
Minimum accessible volume of a channel:
Å3
Minimum percentage of total volume:
%
Get the N largest channels:
channels




PRESET EXAMPLES:   
   



Channel Finder – possible the most useful program here. The channel finder can pull interesting channels out from a structure. For example, the exit tunnel from the ribosome, the internal cavity of GroEL and many others. Channel finder works by calculating the shell volume (A) and then subtracts the solvent-excluded volume (B) from the shell volume (A) the resulting volume is the solvent volume (C). Next it only takes the solvent volume that is connected to a point specified by you.




Citation:
'3V: cavity, channel and cleft volume calculator and extractor' (free text)
Nucleic Acids Res. 2010 July 1; 38(Web Server issue): W555–W562
by Neil R. Voss and Mark Gerstein
Download source code
Help
Site news and updates
If you find this useful or want more functionality please contact Neil <vossman77 [at] yahoo.com>
back to main page