Re: [ccp4bb] site mutation evaluation

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

Previous message:
Subject: Re: site mutation evaluation
From: Hongmin Zhang hongmin {- at -} RED {- dot -} DFCI {- dot -} HARVARD {- dot -} EDU
Date: 2008-12-02

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Subject: Re: site mutation evaluation
From: Hongmin Zhang hongmin {- at -} RED {- dot -} DFCI {- dot -} HARVARD {- dot -} EDU
Date: 2008-12-03

Subject: Re: site mutation evaluation
From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2008-12-03

In that case you might want to use CNS with model_anneal.inp or
model_minimize.inp, or the equivalents in phenix

Jürgen

On 2 Dec 2008, at 21:29, Hongmin Zhang wrote:

> Yes, it is better to have MD or energy minimization. Otherwise, with
> only view on the screen, we can't tell if the mutated residue would
> disturb ligand binding because of the side chain flexibility.
> Best!
> Hongmin
>
> On Wed, Dec 3, 2008 at 12:50 PM, Juergen Bosch
> > wrote:
> Pymol
> the question is, into how much trouble do you want to get ?
> MD simulations ? Energy minimisation ? Then you will need to do more
> than just mutate on the sreen one residue with Pymol.
>
> Jürgen
>
> On 2 Dec 2008, at 17:29, Hongmin Zhang wrote:
>
> Dear All,
> I am trying to mutate a single amino acid in a PDB to see if the
> mutant
> disturbs ligand binding. Does anyone know any software that can do
> such work?
> Thanks a lot!
>
> -
> Jürgen Bosch
> University of Washington
> Dept. of Biochemistry, K-426
> 1705 NE Pacific Street
> Seattle, WA 98195
> Box 357742
> Phone: +1-206-616-4510
> FAX: +1-206-685-7002
> Web: http://faculty.washington.edu/jbosch
>
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-
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone: +1-206-616-4510
FAX: +1-206-685-7002
Web: http://faculty.washington.edu/jbosch

CCP4bb navigation

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

Previous message:
Subject: Re: site mutation evaluation
From: Hongmin Zhang hongmin {- at -} RED {- dot -} DFCI {- dot -} HARVARD {- dot -} EDU
Date: 2008-12-02

Next message:
Subject: Re: site mutation evaluation
From: Hongmin Zhang hongmin {- at -} RED {- dot -} DFCI {- dot -} HARVARD {- dot -} EDU
Date: 2008-12-03