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
.