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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