ADL: Docking robustness

Amr AL-HOSSARY amr_alhossary at hotmail.com
Tue Dec 9 14:01:50 PST 2014


Vina is supposed to do a stochastic search using both Monte Carlo and BFGS
methods.
The seed is used to control the randomness by giving a fixed start point if
you need.

I don't see any "issue" there to mitigate.

Amr


-----Original Message-----
From: autodock-bounces at scripps.edu [mailto:autodock-bounces at scripps.edu] On
Behalf Of Dariush Mohammadyani
Sent: Tuesday, December 09, 2014 5:28 AM
To: autodock at scripps.edu
Subject: ADL: Docking robustness

Hello All,

I am wondering to know why changing the seed (using -seed option) results in
significantly different results.
For instance, in one docking most of 9 models may represent a binding pose,
which can be different from the results of another docking using different
random seed number.

How can I mitigate this issue?

Thank you for answering!

Regards,
Dariush
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