Re: [ccp4bb] Cavity filling

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Judging a homology model
From: Raja Dey deyraja1 {- at -} YAHOO {- dot -} CO {- dot -} IN
Date: 2010-01-06

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From: Francois Berenger berenger {- at -} RIKEN {- dot -} JP
Date: 2010-01-06

Subject: Re: Cavity filling
From: Oliv Eidam oliv {- dot -} eidam {- at -} GMAIL {- dot -} COM
Date: 2010-01-06

Hi Simon,

I suggest docking with the free web service DockBlaster:
http://blaster.docking.org/start.shtml
DockBlaster runs DOCK 3.5.54 and gives you the freedom to dock any molecule
you want into your structure.
Check out this page for more information:
http://wiki.compbio.ucsf.edu/wiki/index.php/DOCK_Blaster:FAQ

All you need is a PDB file as input. After the preparation step, you can
choose what library you want to dock. A library of interest for you is the
fragment-like molecule library of ZINC (http://zinc.docking.org). Currently,
it contains 458080 purchasable molecules with MW<250Da.

It should be docked within a couple of days and and give you an idea what
kind of molecules might fit into your pocket.

Good luck,

Oliv

On Wed, Jan 6, 2010 at 5:08 AM, Simon Kolstoe wrote:

> Dear ccp4bb
>
> A structure I have recently finished has a cavity with four waters in it. I
> am wondering if I might be able to fit a small molecule in the same place.
> Does anyone know a way of making some type of map of this cavity and then
> searching through a small molecule library to see what might fit in it (I'm
> guessing there is commercial software that will do this however I am after
> something without large financial commitments!)?
>
> Thanks,
>
> Simon
>

--
Oliv Eidam, Ph.D.
Postdoctoral fellow

University of California, San Francisco
Dept. of Pharmaceutical Chemistry
1700 4th Street, Byers Hall North, Room 501
San Francisco, CA 94158 - Box 2550

Phone: 415-514-4253
Fax : 415-514-4260
Email: eidamo@blur.compbio.ucsf.edu

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Judging a homology model
From: Raja Dey deyraja1 {- at -} YAHOO {- dot -} CO {- dot -} IN
Date: 2010-01-06

Next message:
Subject: open source project announce: parallel/distributed execution of commands
From: Francois Berenger berenger {- at -} RIKEN {- dot -} JP
Date: 2010-01-06