Re: [ccp4bb] Cavity filling

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

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

Previous message:
Subject: Re: Reg. Protein purification
From: Jurgen Bosch jubosch {- at -} JHSPH {- dot -} EDU
Date: 2010-01-08

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Subject: Re: Reg. Protein purification
From: Roger Rowlett rrowlett {- at -} COLGATE {- dot -} EDU
Date: 2010-01-08

Subject: Re: Cavity filling
From: Simon Kolstoe s {- dot -} kolstoe {- at -} UCL {- dot -} AC {- dot -} UK
Date: 2010-01-08

Thank you ccp4bb for guidance once again, and especially Jurgen Bosch
for suggesting Voidoo and Oliv Eidam for suggesting Dockblaster.

I was able to use Voidoo which I already had installed from USF to
better define the cavity I was interested in. I then was able to use
the free web server Dockblaster (http://blaster.docking.org/
start.shtml) to screen various sections of the ZINC database and give
me some hits. The trick was to position a phosphate in the middle of
the site defined by voidoo and then give the coordinates of this
"fake" phosphate to Dockblaster in order to define the cavity for the
subsequent docking.

I won't take the results of the in silico docking too seriously as I
have had limited success with similar methods in the past (and the
molecules in the ZINC library are not quite as available as the
library advertises), however it does at least give me a start in
thinking about the sort of molecules that might fit my cavity.

Thanks once again for the help,

Simon

CCP4bb navigation

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

Previous message:
Subject: Re: Reg. Protein purification
From: Jurgen Bosch jubosch {- at -} JHSPH {- dot -} EDU
Date: 2010-01-08

Next message:
Subject: Re: Reg. Protein purification
From: Roger Rowlett rrowlett {- at -} COLGATE {- dot -} EDU
Date: 2010-01-08