Thanks for the quick answer!
Fabian
Dr. Fabian Glaser
Head of the Structural Bioinformatics section
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa 32000, ISRAEL
fglaser at technion dot ac dot il
Tel: +972 4 8293701
http://bku.technion.ac.il
> On 29 Oct 2015, at 5:32 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
> On Thu, Oct 29, 2015 at 11:27 AM, Fabian gmail <fabian.glaser.gmail.com <mailto:fabian.glaser.gmail.com>>
> wrote:
>
>> Hi,
>>
>> I am interested in calculating DDG for WT - MUTANT of a certain multi
>> peptide system (32 identical peptides). But I cannot use the
>> &alanine_scanning procedure in MMPBSA.py since I need to mutate not one but
>> all 32 residues (one in each peptide) including on the ligand and receptor
>> (31 and 1 peptide respectively). That cannot be done with MMPBSA.py I
>> understand, which allows a single mutation.
>>
>> So I thought to repeat the whole MD and MMPBSA.py energy calculations,
>> using a 32 ALA mutant receptor, complex and ligand, and then compare the DG
>> of mutant and WT system (using exactly the same conditions).
>>
>> Is that a reasonable approach?
>>
>
> Yes.
>
>
>
>> I mean will I get reasonable DDG (wt - mutants) prediction difference?
>>
>
> It should be better than alanine scanning in MMPBSA.py since it will add
> the actual protein response to the mutations.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Thu Oct 29 2015 - 09:00:05 PDT
