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

[James Starlight]

Thanks for the suggestions Catarina!

Actually I am not sure regarding accuracy of how the h-bonds and
saltbridges will be modelled during CG simulations :-)
So right now I will be interesting to focus on some very general
sollutions like contact maps, inter-subunit (inter-chain in case of my
system) distances etc

Cheers!

2016-04-27 16:00 GMT+02:00 Catarina A. Carvalheda dos Santos
<c.a.c.dossantos at dundee.ac.uk>:
> 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.
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>
>
>
> --
> Catarina A. Carvalheda
>
> PhD Student
> Computational Biology Division
> SLS & SSE
> University of Dundee
> DD1 5EH, Dundee, Scotland, UK
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