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

James Starlight jmsstarlight at gmail.com
Wed Apr 27 15:42:37 CEST 2016

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!


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