Hi Jacob,
I recommend using specific tools to perform docking. Some options are:
http://rosie.rosettacommons.org/docking/
https://salilab.org/imp/
http://haddock.chem.uu.nl/
Also you could check the Capri <http://www.ebi.ac.uk/msd-srv/capri/> home
page, to have and idea of the different methods and their performance.
Cheers,
Osvaldo.
On Sat, Dec 13, 2014 at 1:47 AM, Jacob Lewis <jl...@uowmail.edu.au> wrote:
Hi all,
>
> I am trying to crudely dock a protein into a complex, one protein contains
> a large loop region that clashes when docked and needs to be moved quite a
> distance. moving it using just individual atoms is extremely difficult and
> frustrating. Does anyone have a sensible solution to move residues in the
> loop while keeping the proper bond/distance restraints for peptide bonds?
>
> Cheers,
>
> Jacob
>
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