Can anyone please explain how to calculate the active site cavity volume of a given protein?

18 August 2017 1 6K Report

I have a set of PDB structures of proteins and I want to calculate cavity volume of each protein. Is there any trusted software or online server for this purpose?

Thanks in advance.

Florent Hédin

You can try GHECOM

http://strcomp.protein.osaka-u.ac.jp/ghecom/

It has the advantage of being relying on a mathematically rigorous definition of the pockets :

check

http://onlinelibrary.wiley.com/doi/10.1002/prot.21283/abstract

and

http://onlinelibrary.wiley.com/doi/10.1002/prot.22639/abstract

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