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 the highest 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 best twenty loops - I plot these data with the DOPE variations and I check a correlation between 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 best 20 (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 blind predictions ?


I am soory for my long list but I am really interested in this problem .

Thank you !

Karol Kaszuba