ADL: Fwd: autodock zinc redocking

Recep adıyaman radiyaman at nku.edu.tr
Wed Apr 16 00:49:16 PDT 2014


Hi

We are doing mutations in metal binding proteins. We would like to compare
binding affinites before and after the mutations.

We are trying to use AutoDock for this purpose, since AutoDock was
mentioned in Daniel Hoffmann's publication "Estimating affinities of
calcium ions to proteins". In that article, they used redocking method.

We picked the Zn atom in wild type protein as center of grid box. Also we
used size 1 for x,y,z. We used the attached conf.txt file.

We are facing a problem in our calculations: the affinity values are always
between 0-2 kcal/mol which is making it difficult to compare results. Also,
we noticed that in Hoffmann's study, AutoDock's affinity values are still
between 0-2 kcal/mol although emprical values are between ~3-14 kcal/mol.
Should we find out a coefficient to convert AutoDock's affinity values to
predict actual value?
Do you have any suggestions for our case?

Researcher Recep ADIYAMAN
Namik Kemal University
Distance Education Center
+905397611054
+902822501071 Tekirdağ-TÜRKİYE
recepadiyaman2244 at gmail.com
radiyaman at nku.edu.tr
radiyaman.nku.edu.tr <radiyaman at nku.edu.tr>


More information about the autodock mailing list