Hi Hongmin,
That should need some docking softwares or the structures of the complex.
ta
liu
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 <[log in to unmask]
> <mailto:[log in to unmask]>> 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
>> <[log in to unmask] <mailto:[log in to unmask]>> 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
>
>
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