When you say you want an easy-to-get-easy-to-use binding energy/contact
area calculator I assume you mean a simple scoring function.
I have suggested that such functions cannot achieve reliable, accurate
general
affinity estimation (pdfs sent separately), and so far this seems to
be borne out (see Marsden et al, Org. Biomol.Chem. 2, 3267 (2004)).
For a web-based score try this:
http://www.scfbio-iitd.res.in/software/drugdesign/bappl.jsp
or this:
http://www.agklebe.de/affinity
No warranty or recommendation implied! I have not used either site.
Please use any such tools with caution. All the empirical scoring
functions i have come across ignore water and protein dynamics (as
well as pH, temperature, ionic strength, cosolvents, water activity....)
good luck
Jeremy
Yokohama
On Feb 22, 2007, at 3:32 AM, Xu TAN wrote:
Hi, all
Does anybody have experience with binding energy calculation of
ligand-protein
interaction? What are the good programs out there ? I am aware of
several such
as AutoDock, Dock, Tinker, but they seem to be made for docking, I am
looking for
easy-to-get-easy-to-use binding energy/contact area calculator.
Thanks for all you input !
Xu Tan
University of Washington, Seattle
