Binding points

Leleonidas · **Joined:** Tue Jul 27, 2010 3:00 pm **Posts:** 2

I made a dock between an enzyme and a knewn inhibitor and find binding points.
But the ligand i use is known to be toxic.

How can i generate others ligands able to binds to the same points (with the hope to fiond ligands not toxic) ? :?:

bikadi · **Joined:** Wed Oct 29, 2008 2:24 pm **Posts:** 204

The question is rather a chemistry question than a docking issue, if I understand well. The question is, what is the origin of the toxicity of the ligand - inhibiting the protein in question or interacing with other proteins. If the toxicity comes from the interaction with the protein used in docking, then I feel the ligands are either toxic or binds weekly. If the reason of toxicity is not related to the protein in question, than virtual high throughput screening can be the solution - docking thousands of ligands to the same binding site and filtering to the same interaction. We are currently working on this kind of server, which will be released this year.

Kind Regards,
Zsolt

Leleonidas · **Joined:** Tue Jul 27, 2010 3:00 pm **Posts:** 2

Thank you very much.Yes in this case the ligand is known to be a "poison" for the whole organism.

I"ll wait for the release of the new server.

alieen · **Joined:** Thu Nov 20, 2014 10:01 am **Posts:** 1

For the brief time you were makeing the reports in PDF it was greatly appreciated. It helped out in my analysis of the data tremendously. I was wondering if that feature would be possible to begin again.

Thanks

____________________________

emma

bikadi · **Joined:** Wed Oct 29, 2008 2:24 pm **Posts:** 204

We are still making pdf reports. Please send me a docking result link where you cannot find it.

alieen wrote:

For the brief time you were makeing the reports in PDF it was greatly appreciated. It helped out in my analysis of the data tremendously. I was wondering if that feature would be possible to begin again.

Thanks

____________________________

emma