The copy selection process
Each MC2 run is divided into five Monte Carlo cycles of identical size, typically 20,000 steps for the test system.
The selection of optimal loop copies takes place at the end of each cycle in accordance with the energy associated with each copy. It is necessary to sufficiency explore the conformational space between the partners and the side-chains conformation before restrict the number of copies which will represent the loop in the next cycle. If the step number is too low, the system will converge too rapidly toward a solution that will be not necessary the good one.
The copy weights Ck associated with the k copies are initially all set to 1/N (N is the number of loop copies). At the end of each MC2 cycle, they are adjusted on the basis of the partial energy Ek averaged over the cycle. Adjustement is performed following the Boltzmann probability Pk:
R is the gas constant and Teff is an effective temperature that regulates the degree of discrimination between the copies. The weights of the copies are deduced from the probabilities Pk by normalization: The degree of discrimination of loop copies, and thus the choice of the effective temperature Teff is a key element of the method.
Docking macromolecules with flexible segments.
Bastard K, Thureau A, Lavery R, Prevost C.
J Comput Chem. 2003 Nov 30;24(15):1910-20. (pubmed)