Hello,
I am writing a paper on tunnels for small molecule access to buried
active sites in proteins. I have noticed that tunnel prediction programs
like CAVER and MOLE predict tunnels that align pretty well with the
interior cavities displayed by Pymol. However, the size of the cavities
predicted by Pymol are generally bigger than the diameter of the tunnel
predicted by CAVER/MOLE, even after adjusting for probe size. My question
therefore is "What type of algorithm (grid based, sphere based, etc) is
used by Pymol to detect cavities?". Since the corroboration of tunnels
predicted by CAVER and interior cavities predicted by Pymol bolster the
computational prediction of tunnels, I would like to add this dual method
to the paper. But I would need to account for the discrepancy in diameter.
I hope that someone would be able to help me with an answer.
Best wishes. And a happy new year.
Rahul Banerjee
University of Minnesota
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