Should one put position restraint on protein backbone during simulations?

31 July 2020 1 3K Report

Hi,

I am studying a transporter protein. X ray crystallographic structure is not known yet. So, i am using homolgy modelled structures for my studies. I am curious if i should put position restraints on my protein backbone during simulation run? or should i leave it free to adjust itself. what approach is better to get reliable protein architecture and study dynamics?

Yogesh Sharma

Suji George sir, iam asking in production run . should one restrain protein backbone in production run? as one would have homology modelled structure already and leaving that structure free might alter structure from modelled confirmation.

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