What are the different ways to evaluate a loop in a homology modelor loop modelling?
Priyanka Suryadevara
First step to be done is to check whether any of the residues of the particular loop fall in the disallowed region in Ramachandran Plot. If all the residues are in allowed region, it can be an acceptable model.
Second thing can be done by comparing the loop region present in the template by correlating with its B factor.
Molecular dynamics simulations can finely explain the loop behaviour under a precise force field.
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