Subject: Is Auotdock self sufficient?

From: Prashant Desai <[email-masked]>
Date: Sat, 24 Mar 2001 23:03:01 +0530

I tried understanding DOCK and  I realized that one requires 'MS' from
QCPE to generate molecular surfaces. Since I don't have 'MS' can anybody
suggest some way out?
How about using Autodock? Is it self sufficient or even it requires use
of some additional softwares?
I am also looking for performance comparison of 'Affinity' from MSI with
other docking packages. I have not come across as many references on use
of Affinity as those for either DOCK or Autodock. Can anyone send me a
list of articles where Affinity has been utilized or even compared with
other docking softwares?
Thanking in advance.
Prashant Desai

---

From: "art'" <[email-masked]>
Date: Fri, 23 Mar 2001 22:25:39 +0100

Hi Desai,

AutoDock has almost all software to make docking, with exception :
1. To visualize the structures in PDB (the results)
2.To create PDBQ file for ligand and macromolecule (add charges to PDB format).
Of course, here we need some force field to calculate charges .......

The latest thing make the most inconvenience to prepare jobs ... And 'addsol'
crashes while converting  PDBQ to PDBQS file. Here I've wrote my own win32
application.

I don't know about DOCK, but AutoDock have rised some doubts about flexible
docking. If anybody has the experience of flexible docking with AotoDock 3.0, it
would be nice if one could share his/her comments about that . :)

have a good day
A.Ziemys

Prashant Desai wrote:

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---

From: "Garrett M. Morris" <[email-masked]>
Date: Sat, 24 Mar 2001 09:37:47 -0800

Dear Prashant,

With the release of AutoDockTools, also known as 'ADT', AutoDock has
become more self-sufficient than ever.  ADT provides a graphical user
interface to set up the ligand PDBQ file, the AutoGrid grid maps, the
AutoDock docking parameters, the ability to launch docking jobs, and
the ability to read in and analyse DLG AutoDock docking log files. You
can visualize isocontoured AutoGrid maps for atomic affinity and
electrostatice potential, and compute and display molecular surfaces.

Babel has been ported into ADT, so its Gasteiger partial atomic charge
calculation method is available for small molecules, and there is also
the ability to assign Kollman united-atom charges to
proteins.  Previously, you would have needed SYBYL to do this.

You can also assign solvation parameters to a macromolecule, and
perform operations like adding hydrogens and merging non-polar
hydrogens, or detecting aromatic carbons (necessary for solvation
parameters).

ADT is free for non-commercial applications, and is available from Art
Olson's Molecular Graphics Laboratory web site - click on Python
Software Development's "Related links", then "Downloads"

http://www.scripps.edu/pub/olson-web/index.html

After you have accepted the license agreement and registered (free),
click the radio button "Download Python packages" and then click
"Start".

Currently supported platforms are:

	SGI    IRIX 6.2 or higher, R4000 or better
	Intel  Linux 2
	Sun    Sun OS 5

Coming soon:

	Windows
	Mac OS X 10.0

You can select all the packages you want and the packager will tar
everything you need into one downloadable file.   Just check the
"AutoDockTools" check-box and then click "Select dependent
packages".  The packager determines any dependencies for you.

On Fri, 23 Mar 2001, art' wrote:

> 1. To visualize the structures in PDB (the results) 2.To create
> PDBQ file for ligand and macromolecule (add charges to PDB
> format). Of course, here we need some force field to calculate
> charges .......
> 
> The latest thing make the most inconvenience to prepare jobs ...
> And 'addsol' crashes while converting PDBQ to PDBQS file. Here

Email Ruth Huey if you have problems with "addsol" - her email address
is [email-masked]; this may have already been fixed in the
currently released tar file.

> I've wrote my own win32 application.
> 
> I don't know about DOCK, but AutoDock have rised some doubts about
> flexible docking. If anybody has the experience of flexible
> docking with AotoDock 3.0, it would be nice if one could share
> his/her comments about that . :)

Take a look at the paper in the Journal of Computational Chemistry
comparing Simulated Annealing, Genetic Algorithm and Lamarckian
Genetic Algorithm in AutoDock 3.0:

Morris, G. M.,  Goodsell, D. S.,  Halliday, R.S.,  Huey, R.,  Hart,
W. E.,  Belew, R. K.  and  Olson, A. J.  (1998), J. Computational
Chemistry, 19: 1639-1662. 
"Automated Docking Using a Lamarckian Genetic Algorithm and and
Empirical Binding Free Energy Function". 

AutoDock's web site is at:

http://www.scripps.edu/pub/olson-web/doc/autodock/

For more information and a list of peer-reviewed publications, click
on "References".

> Ftp: ftp.ccl.net  |  WWW: http://www.ccl.net/chemistry/   | Jan: [email-masked]

Happy docking!

Garrett

___
Dr Garrett M. Morris, MA, DPhil
The Scripps Research Institute,       tel: (858) 784-2292
Dept. Molecular Biology,  MB-5,       fax: (858) 784-2860
10550  North Torrey Pines Road,       email: [email-masked]
La Jolla,  CA 92037-1000,  USA.       www.scripps.edu/pub/olson-web/gmm