I built a model using swiss model web server from a template and the Ramachandran plot contained some outliers in the active site.
My question is, which process should I use to solve this, minimization or refinement, and what is the difference between them?
Jitesh Doshi
Minimization is one of the ways to refine the model structure. Apart from energy minimization, protein can be refined using cleaning (geometry optimization), manual editing of torsions of outlier residues, molecular dynamics etc... You can go for minimization of your model for most common applications
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