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

Catarina A. Carvalheda dos Santos c.a.c.dossantos at dundee.ac.uk
Wed Apr 27 16:01:07 CEST 2016

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.


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.
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Catarina A. Carvalheda

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

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