binding sites

cindrella1 · **Joined:** Sat Mar 26, 2011 5:17 am **Posts:** 2

dear sir,

after protein is prepared it will be better to provide automatic active site of protein where ligand can bind and can be seen for inhibition and also it will be better to find a way whether the ligand identified is activator also.if we can upgrade this type of mechanism in docking it will be better.

hoping reply from you

thank you for docking server for doing excellent service

bikadi · **Joined:** Wed Oct 29, 2008 2:24 pm **Posts:** 209

Hello,

thank you for your comments. We are considering some type of automated binding site recognition. Right now the binding site of the x-ray ligand is selected by default. The problem with site finders is that they are either too slow or too unreliable.

As for your second comment, if I understand well, you are looking for a prediction with more explicit result on biology (e.g. to predict being inhibitor). We are just working on a product capable of doing this.

Kind Regards,
Zsolt Bikadi

vermapooja74 · **Joined:** Tue Jul 10, 2012 9:25 am **Posts:** 1

hello,
Is it possible to perform docking at specific site defined by the user????????

hazaie · **Joined:** Wed Oct 29, 2008 2:24 pm **Posts:** 40

Hello,

of course, this is possible, the site can be defined in the select simulation box step.

Eszter