saccenti@cerm.unifi.it 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 -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage