Hello, I generated 500 loops for two segments - each one 8 residues long.I choose the best 20 loops - the lowest DOPE. A DOPE difference between thehighest energy loop and the lowest energy one is 130.My questions are: 1) Can I simply choose the lowest energy loops as a native loops ? 2) Can I choose my best loops in a following way: - I assign the template loops as a reference structures - I calculate local RMSD (N, Calfa, C, O - only on the loop) for the besttwenty loops- I plot these data with the DOPE variations and I check a correlationbetween energy and structural variability 3) Can I choose my best loops in a following way: - I assign the lowest DOPE loops as a reference structures rest of a procedure like in point 2 4) What is an acceptable (aproximately) DOPE difference in a set of the best20 (30) loops between the higest energy loop and the lowest one ? 5) How many stem residues modeller algorithm moves during optimization ? 5) Maybe there is a different way to increase loop credibility in blindpredictions ? I am soory for my long list but I am really interested in this problem. Thank you ! Karol Kaszuba