Is there any further way to refine loops of protein, especially which cant be removed from Modloop.
You can do loop refinement using Modeller. The following links are few other options.
http://galaxy.seoklab.org/cgi-bin/submit.cgi?type=LOOP
http://spdbv.vital-it.ch/loop_tut.html
https://salilab.org/modeller/manual/node33.html
https://omictools.com/protein-loop-modeling-category
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