F 2000 1500 1000 500

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 Building block test

Figure 19.8 (a) One algorithm node experiment and (b) two algorithm node experiment.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 Building block test

Figure 19.8 (a) One algorithm node experiment and (b) two algorithm node experiment.

19.6.3 Building Block Size Analysis

The BB analysis is performed in an attempt to identify the building block sizes that result in finding better solutions for POLY. A BB is a partial string representing bits from one, some, or all of the dihedral angles that each chromosome represents [49]. The BBs are not restricted to be contiguous bits from the chromosomes but instead can be noncontiguous bits from the chromosome. This analysis covers a variety of BB sizes and compares the results to determine which size produces the best statistical results. The BB ranges chosen for testing included: 16-18, 18-20, 20-22, ... , and 38-40.

The results of the BB size experiment show that BB sizes of 30-32 yielded the best results for POLY. Although, this BB size is specific for POLY, it should apply to other proteins having an alpha-helical structure. Additionally, BB size 30-32 yielded the best overall fitness value found during all of the BB testing of -140 kcal, which is in the neighborhood of the accepted CHARMm fitness for this protein.

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