AN ALGORITHM FOR AUTOMATICALLY GENERATING PROTEIN TOPOLOGY CARTOONS

An algorithm is described for automatically generating protein topolog y cartoons. This algorithm optimally places circles and triangles depi cting alpha-helices and beta-strands respectively giving a pictorial t opological summary of any protein structure. Beta-Sheets, sandwiches a nd barrels are automatically identified and represented using special templates. The output from this algorithm may be controlled by adjustm ent of variable weights during the optimization step giving a preferre d result. The rules for generating protein toplogy cartoons, including consideration of the handedness of local structure motifs, are discus sed. The design of this algorithm is completely general and is easily adapted to include further rules that dictate the generation of the ca rtoons.