I prepared de novo model of two different proteins using I-TASSER online server and went for docking with best result for interaction study among those proteins.
I already confirmed the interaction of those proteins with co-immunoprecipitation studies in wet lab. Now, can anyone suggest how to go about the simulation of this structure?
Is it important for that? if Yes, then why? At least for the publication point of view. My main experiments are related to wet lab, I just want to use these data as supplementary information.
Dear Soni Shaikh,
I-TASSER is a good server for protein model and currently lots of publications are being published using this online server. Molecular Dynamics Simulation (MDS) is one of the best approach to get an insight into the molecular interaction and to evaluate the molecular stability of the modeled protein. Most of the researchers use this approach for their research papers But since you have done wet lab experiment and you just want to put it as a supplementary work..it is not necessary for you to go for MDS. It will consume more than two months in local configured system. You can simply evaluate your protein based on the Procheck, Whatif server, Errate and Verify3D.
StIll if you want to use MDS. I will suggest you to use GROMACS4.5, which is freely available at www.gromacs.org you can download the software and install it. The installing procedure is available at http://www.gromacs.org/Documentation/Installation_Instructions. and gromacs tutor is availabe at http://www.google.co.in/url?sa=t&rct=j&q=&esrc=s&frm=1&source=web&cd=5&ved=0CE0QFjAE&url=http%3A%2F%2Fwww-personal.umich.edu%2F~amadi%2Ffwspidr_tutor.pdf&ei=NQV5UPufMoPyrQfIqIHQAg&usg=AFQjCNHZWOp7mz9fYisxaGzJNhCablQbYw&sig2=ZL7QFqnYMOtM3IR27aLQHQ.
Importance of simulation is purely based on scope ur work, its very specific.. If ur work is just to show the interaction, its not mandatory to perform simulation but if ur work is to understand the interaction then simulation can give more structural insights in understanding the stability and flexibility and nature of interaction at atomic level.
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