During the first cycle of MC2 simulation,
repulsive energy terms dominate: as a result, the copies which do not interact
with the ligand are favored over copies with potential surface complementarity
with the ligand. This problem has been resolved by reducing the repulsive
van der Waals contribution to the total energy score and by adding a low
contact penalty during copy selection.
The loop copies which do not interact with the ligand are in green, the loop copies with potential surface complementarity are in blue
(the copy nearest the cristallographic loop are in cyan). The ligand (DNA) is in red.
with flexible segments.
Bastard K, Thureau A, Lavery R, Prevost C.
J Comput Chem. 2003 Nov 30;24(15):1910-20. (pubmed)