Hi there
Assuming you have a model of the complex you are interested in
tinkering with, try submitting it to the Rosetta Alanine Scanning
servery thing.
http://robetta.bakerlab.org/alascansubmit.jsp
By default, it mutates each residue in the interface to ala, does some
local minimisation (side chains only, I seem to recall) and then re
calculates the binding energy. You can also give it lists of other
mutants to try.
If your data is sensitive , you can download the rosetta software and
do it yourself - the rosetta software is a little complicated
sometimes though.
HTH,
David.
2008/12/3 junfeng liu <[log in to unmask]>:
> 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
>>
>>
>
--
============================
David C. Briggs PhD
Father & Crystallographer
http://drdavidcbriggs.googlepages.com/home
AIM ID: dbassophile
============================
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