wrote:
Which is the best strategy to assess the quality of a model and sort them out of a bunch of many calculated models? I have models a complex of two proteins plus a metal ion.
Of the methods we have available in Modeller, DOPE is probably the most reliable - although as a statistical potential, it won't score your metal ion at all. See http://salilab.org/modeller/9v2/manual/node29.html for an example.
Ben Webb, Modeller Caretaker
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