Assuming you have a model of the complex you are interested in
tinkering with, try submitting it to the Rosetta Alanine Scanning
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
2008/12/3 junfeng liu <[log in to unmask]>:
> Hi Hongmin,
> That should need some docking softwares or the structures of the complex.
> Hongmin Zhang wrote:
>> Thanks! I think we still can't tell if the mutant would disturb ligand
>> binding or not.
>> 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
>> 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
>>> On Wed, Dec 3, 2008 at 12:50 PM, Juergen Bosch
>>> <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>>> 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.
>>> 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
AIM ID: dbassophile