Re: [ccp4bb] site mutation evaluation

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

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Subject: Re: Temperature factor discrepancy
From: Dirk Kostrewa kostrewa {- at -} LMB {- dot -} UNI-MUENCHEN {- dot -} DE
Date: 2008-12-03

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From: Valerie Biou biou {- at -} LEBS {- dot -} CNRS-GIF {- dot -} FR
Date: 2008-12-03

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

Eventually you will have to make the mutant for a reviewer. So in
silico will only give you perhaps some ideas but there's no way of
avoiding wetlab.

Jürgen
On 2 Dec 2008, at 22:38, Hongmin Zhang wrote:

> Thanks! I think we still can't tell if the mutant would disturb
> ligand binding or not.
> Best!
> Hongmin
>
> On Wed, Dec 3, 2008 at 2:15 PM, Juergen Bosch
> wrote:
> 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
>
>

-
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: Temperature factor discrepancy
From: Dirk Kostrewa kostrewa {- at -} LMB {- dot -} UNI-MUENCHEN {- dot -} DE
Date: 2008-12-03