ADL: Automating docking

Jeffrey Dyason j.dyason at griffith.edu.au
Mon Apr 2 14:22:53 PDT 2007


John,
        There are some scripts used by ADT which can be called from the 
command line to automate ligand setup 
($MGL_ROOT/share/lib/python2.4/site-packages/AutoDockTools/Utilities24/prepare_ligand.py). 
Look for others in this directory. Or the following journal article 
describes a method of doing what you want to do and they provide the 
required software.


Vaque, M.; Arola, A.; Aliagas, C.; Pujadas, G. BDT: an easy-to-use 
front-end application for automation of massive docking tasks and complex 
docking strategies with AutoDock. Bioinformatics 2006, 22, 1803-1804. 
MOTIVATION: AutoGrid/AutoDock is one of the most popular software packages 
for docking, but its automation is not trivial for tasks such as (1) the 
virtual screening of a library of ligands against a set of possible 
receptors; (2) the use of receptor flexibility and (3) making a 
blind-docking experiment with the whole receptor surface. This is an 
obstacle for research teams in the fields of Chemistry and the Life 
Sciences who are interested in conducting this kind of experiment but do 
not have enough programming skills. To overcome these limitations, we have 
designed BDT, an easy-to-use graphic interface for AutoGrid/AutoDock. 
AVAILABILITY: BDT is available for free, upon request, for non-commercial 
research.


Bye Jeff.
-----------
Jeff Dyason                                    e-mail: 
J.Dyason at griffith.edu.au
Institute for Glycomics http://www.griffith.edu.au/glycomics
Griffith University                          (Gold Coast Campus)  
PMB 50 Gold Coast Mail Centre       Tel: +61 7 5552 7028
Queensland 9726 Australia              Fax: +61 7 5552 8098



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Date: Mon, 2 Apr 2007 11:01:10 -0500
From: "Beale, John" <jbeale at stlcop.edu>
Subject: ADL: Automating docking
To: <autodock at scripps.edu>
Message-ID: <C673A3184774564799BB801ED479817E2B1C36 at mail.stlcop.local>
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This is probably a pretty simple question, but I am new to Autodock and
haven't figured this out (I am using Autodock tools). I can easily do
the docking for individual molecules one at a time. How can I automate
the process so that Autodock performs docking calculations on a series
of congeners from a list of structures? For instance, I would like to
perform docking experiments on a series of beta-lactam antibiotics with
penicillin binding proteins without having to manually enter each
ligand. I am sure that there must be a way to do this with Autodock, but
I just don't see it. I would appreciate any help that I can get.





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