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Bulletin of the Korean Chemical Society (BKCS)

ISSN 0253-2964(Print)
ISSN 1229-5949(Online)
Volume 21, Number 3
BKCSDE 21(3)
March 20, 2000 

Comparison of Recombination Methods and Cooling Factors in Genetic Algorithms Applied to Folding of Protein Model System
Soohaeng Yoo, DooIl Kim, Sun-Hee Jung*
We varied recombination method of genetic algorithm (GA), i.e., crossover step, to compare efficiency of these methods, and to find more optimum GA method. In one method (A), we select two conformations (parents) to be recombined by systematic combination of lowest energy conformations, and in the other (B), we select them in a ratio proportional to the energy of the conformation. Second variation lies in how to select crossover point.First, we select it randomly (1). Second, we select range of residues where internal energy of the molecule does not vary for more than two residues, select randomly among such regions, and we select either the first (2a) or the second residue (2b) from the N-terminal side, or the first (2c) or the second residue (2d) from the C-terminal side in the selected region for crossover point. Third, we select longest such region, and select such residue (as cases 2) (3a, 3b, 3c or 3d) of the region. These methods were tested in a 2-dimensional lattice system for 8 dif-ferent sequences (the same ones used by Unger and Moult., 1993). Results show that compared to Unger and Moult's result (UM) which corresponds to B-1 case, our B-1 case performed similarly in overall. There are many cases where our new methods performed better than UM for some different sequences. When cooling factor affecting higher energy conformation to be accepted in Monte Carlo step was reduced, our B-1 and other cases performed better than UM; we found lower energy conformers, and found same energy conformers in a smaller steps. We discuss importance of cooling factor variation in Monte Carlo simulations of protein folding for different proteins. (A) method tends to find the minimum conformer faster than (B) method, and (3) method is superior or at least equal to (1) method.
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