ADL: screening with small molecule present

Brian Moldover moldoverb at gmail.com
Tue Dec 10 06:49:21 PST 2013


I did screens where ATP was bound and it worked perfectly well. I have not
done any where there is ligand-ligand interaction, but I see no reason why
it wouldn't work. You could always pull it into PyMol afterwards and look
for polar interactions, etc. I know that works. You should try and keep the
search space under 27000 Angstroms (30x30x30) but you can search larger
space if you increase exhaustiveness. 

If you do a fragment screen with an already docked fragment, can you let me
know how well that worked? We've talked about doing that, but most of the
people I work with are limited to screening compounds that they can purchase
commercially. 

-Brian

Chemalytics, Inc. 
Brian Moldover, Ph.D. 
1725 Fairmount Ave.
Philadelphia, PA 19130
Office: 267.639.4787
Mobile: 215.687.3024


-----Original Message-----
From: autodock-bounces at scripps.edu [mailto:autodock-bounces at scripps.edu] On
Behalf Of Michael Osborne
Sent: Tuesday, December 10, 2013 9:38 AM
To: autodock at scripps.edu
Subject: Re: ADL: screening with small molecule present

Hi Brian
Pretty much the same; I want to dock close to the ligand, maybe even detect
interactions with the ligand (a virtual fragment screen with the first
fragment present). I thought about trying to dock around the ligand, but
figured I would need to define more than one grid, as the ligand is quite
large and was not sure this was possible.
Thanks for the speedy reply.
Cheers
Mike

On 10/12/13 9:24 AM, Brian Moldover wrote:
> I've done it with a cofactor still in place, but I am docking outside 
> of that region. What exactly are you trying to do?
>
> -----Original Message-----
> From: autodock-bounces at scripps.edu 
> [mailto:autodock-bounces at scripps.edu] On Behalf Of Michael Osborne
> Sent: Tuesday, December 10, 2013 9:19 AM
> To: autodock at scripps.edu
> Subject: ADL: screening with small molecule present
>
> Hi Everyone
> I was wondering if it anyone has tried to use VINA or autodock to 
> perform a virtual screen against a protein and a small molecule 
> already present (and keeping that molecule there).
> Thanks in advance
> Mike
>
> --
> Mike Osborne
> Iric-Institut de Recherche en Immunovirologie et Cancérologie 
> Université de Montréal
> Ph: (514) 343 6111 ext. 0534(NMR)/ 06070(Office)/ 0610(Wet lab)
> Fax: (514) 343 5839
>
> ________________________________________________
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> ________________________________________________
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--
Mike Osborne
Iric-Institut de Recherche en Immunovirologie et Cancérologie Université de
Montréal
Ph: (514) 343 6111 ext. 0534(NMR)/ 06070(Office)/ 0610(Wet lab)
Fax: (514) 343 5839

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