Dear All,
I would like to study the evolution of local interactions in the particular regions of the protein over the dynamic trajectory. Could you please help me out with the suitable suggestions.
Thanks
with regards
Kesavan
you can use the InterEvDock2 web interface at http://bioserv.rpbs.univ-paris-diderot.fr/services/InterEvDock2/. This server is an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs
or you can use RosettaDock server for local protein–protein docking
If I understand the question correctly, you want to plot a certain value for this "interaction" (angle, distance probably ?) in time. To answer this question it is important to know which MM Force Field you used for the MD simulation ?
Dear Michiel,
You were correct and the MM force field used was MEDUSA for the simulation.
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