[gmx-users] Analysis of the protein-protein binding

[Catarina A. Carvalheda dos Santos]

Hi James,

Trajectory analysis are highly dependent on the system of study, namely on
what you want to get from your simulations. Also, the protocol you
described is a fairly common one.
Having said that, a good strategy is probably starting by checking the
literature for ways to caracterize binding interfaces from simulations for
example (atomic distances, number of contacts, interprotein salt-bridges
and H-bonds, etc...).
Without knowing the details of your system is very difficult to give you
any non-generalist ideas, and you are basically asking GROMACS users to do
your work for you.

Cheers,


On 27 April 2016 at 14:42, James Starlight <jmsstarlight at gmail.com> wrote:

> Dear Gromacs Users!
>
> I am looking for some non-complicated analysis of protein-protein
> association simulation.
> Firstly using MARTINI model I have simulated association between water
> soluble protein and some water-exposed part of the membrane protein
> mediated mainly by the electrostatics attraction between both. Now
> assuming that I have collected 10 trajectories corresponded to 10
> independent MD runs of that process I am looking for some analysis
> method e.g to cluster the binding interfaces occurred during those
> runs. to characterize precisely residues which are crucial for binding
> etc. Will be thankful for any suggestions regarding realization
> assuming that in my model I have big membrane protein consisted of 12
> independent chain in Gromacs topology and small water soluble protein
> defined as independent chain. The brief vizualisation of that I am
> looking to analyze is available here https://youtu.be/u3vKKBq4G6s :-)
>
> Thanks for the help!
>
> J.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>



-- 
Catarina A. Carvalheda

PhD Student
Computational Biology Division
SLS & SSE
University of Dundee
DD1 5EH, Dundee, Scotland, UK