Re: [ccp4bb] site mutation evaluation

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

Previous message:
Subject: Re: site mutation evaluation
From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2008-12-02

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

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

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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CCP4bb navigation

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

Previous message:
Subject: Re: site mutation evaluation
From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2008-12-02

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