First of all you should inspect literature to answer the questions
1) what is the pH-optimum of protein
2) are there any histidines or residues with unusual pK in the region
of your interest.
After that you either add hydrogens automatically by tleap or specify
protonation state of some residues explicitly (taking into account
literature data or predictions given by program calculating pK such as
PROPKA or H++).
On Wed, Apr 13, 2011 at 11:32 PM, Fernando Blanco <amberfbv.gmail.com> wrote:
> Thank you so much
>
> My doubt (as a begginer)
> is how determine which protonation states, and other factors
> are the correct for my protein
>
> The software and the tutorias recommended are great
>
> Fernando
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>
--
Dmitry Nilov,
Faculty of Bioengineering and Bioinformatics,
Lomonosov Moscow State University
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Received on Wed Apr 13 2011 - 23:00:02 PDT
