COMPARISON OF PROTEIN SURFACES USING A GENETIC ALGORITHM

A genetic algorithm (GA) is described which is used to compare the sol vent-accessible surfaces of two proteins or fragments of proteins, rep resented by a dot surface calculated using the Connolly algorithm. The GA is used to move one surface relative to the other to locate the mo st similar surface region between the two. The matching process is enh anced by the use of the surface normals and shape terms provided by th e Connolly program and also by a simple hydrogen-bonding descriptor an d an additional shape descriptor. The algorithm has been tested in app lications ranging from the comparison of small surface patches to the comparison of whole protein surfaces, and it has performed correctly i n all cases. Examples of the matches are given and a quantitative anal ysis of the quality of the matches is performed. A number of possible future enhancements to the program are described which would allow the GA to be used for more complex surface comparisons.