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We have described previously a measure of protein similarity based on a hard ball model of the position of α-carbon atoms in amino acid residues. A genetic algorithm (GA) is used to search the space of possible alignments to identify the maximum possible volume overlap of one protein with another, with the chromosome in this GA using a simple binary encoding scheme. Here, we extend the measure to take account of the secondary structure elements present within a protein, using an elite generational replacement GA, a steady-state GA and a bit-climber; we also consider the use of a Gray coding scheme. Self-recognition and database searching experiments with structures from the Protein Data Bank show that the bit-climber with a Gray code representation gave the best results of the three search methods that were tested.

A similarity score of protein three dimensional structures by hard ball model using a genetic algorithm (2): Overlapping of helix and sheet portions