Dear Yang,
There are several.
I also commend to you:-

Crystallography Reviews, Volume 15, Issue 4 October 2009 , pages 231 - 259
An evaluation review of the prediction of protonation states in
proteins versus crystallographic experiment  Authors: Stuart J.
Fisher; James Wilkinson; Richard H. Henchman; John R. Helliwell
available at:-
http://www.informaworld.com/smpp/content~db=all~content=a915050320~tab=content~order=page

Best wishes,
John
Prof John R Helliwell DSc

On Thu, Aug 12, 2010 at 6:11 PM, yang li <robertcatru...@gmail.com> wrote:
>
> Hi,
>    Is there any server or program can calculate the theoretic PKa of the 
> protein-DNA complex? Given the structure of the protein and the
> sequence of the DNA. Any suggestion will be appreciated!
> Best
> Yang
>



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