Hi Jeff,
You can compare volume of binding cavities of two proteins. You can quickly
check cavity size in your structure using PDBsum or you can use a program
called viodoo to calculate volume of the cavity.
Following paer can be helpful
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2683046/
Rega
Jef,
PISA will give you the size of the protein-substrate interface, which is
inversely correlated to the solvent exposed surface. Subtracting the interface
surface from the total surface of the substrate will give you an estimate of
the solvent exposed surface.
Best regards,
Herman
-Urspr
