ADL: Autodock, Vina and protein-protein interactions

Jean Dessolin j.dessolin at iecb.u-bordeaux.fr
Sat Apr 5 10:55:52 PDT 2014


Dear Lydie,

you might wish to try Zdock for protein-protein docking. You will find 
it on the web.

Ki calculation is based on a constant number multiplying your energy 
score, which is totally empirical. Thus you might wish to abandon Ki as 
a criterion in the future.

Regards.

Jean

Le 05/04/2014 18:39, Lydie Brisson a écrit :
> Dear all,
> I have several questions about molecular docking.
> - I was used to use Autodock 4.2 that can calculate Ki according to binding energy. So my first question is : is there any possibilities for Vina to do so ?
> - Next, I would like like to study interactions between two proteins. I have tried Autodock 4 : Too much atoms for it and too big grid space file. I have tried Vina : it works but it is very time and processor consuming since my gridspace is bigger than 27000A3. Can anyone give me a program that could do such calculations faster ?
>
> Thank a lot for your future answers !
>
> Lydie
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