ADL: Doubt about AutoDock Vina (Redocking)

Brian Moldover moldoverb at gmail.com
Thu Jan 23 11:04:05 PST 2014


>From a practical standpoint, it is more useful to extract the interacting
residues distances, and angles from the crystallographic structure, and use
that as your reference criteria for tuning parameters for redocking. 

If the goal is to run a virtual screen, then that would be the first step in
establishing a benchmark for docking and modeling novel structures. As has
been discussed, using DUD, or alternative scoring methods such as NNScore
are also useful for this process.

-----Original Message-----
From: autodock-bounces at scripps.edu [mailto:autodock-bounces at scripps.edu] On
Behalf Of Oleg Trott
Sent: Thursday, January 23, 2014 1:48 PM
To: autodock at scripps.edu; Renata Parruca da Silva
Subject: Re: ADL: Doubt about AutoDock Vina (Redocking)

Hi

On Wed, Jan 22, 2014 at 11:26 AM, Renata Parruca da Silva
<renataparruca at yahoo.com.br> wrote:
> Hi, My name is Renata Sakata, I'm PhD student from Unicamp, Brazil. I have
a doubt about Redocking.
> How can I get values asRMSD from reference structure (the ligand in 
> the original crystallographic structure),

For aesthetic reasons, Vina doesn't use reference structures as additional
input. You could calculate the RMSDs between structures with, e.g. Vrms, or
other software (You'd need to split the output first, and convert it to SDF
or another appropriate format).

I believe ADT can do this as well, for a somewhat different definition of
"RMSD". Perhaps Ruth will comment on this.

> Population in the optimum cluster (%), Maximum No. of energy evaluation
and GA runs to perform a docking validation.

Vina doesn't use genetic algorithms. I'm surprised how many people are
confused about this. You can control the time-vs-exhaustiveness trade-off
using the "exhaustiveness" parameter (see the FAQ and the video tutorial).

--
Oleg Trott, Ph.D. (Columbia University)

Staff Scientist in the Olson Lab
The Scripps Research Institute

http://olegtrott.com
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