Comparing objects of different sizes: Treating proteins as strings

For low-resolution force field calculations on proteins, one needs a method to automatically identify weak structural similarities in different molecu les. A method is presented which treats sets of three-dimensional coordinat es as graphs, and generates a similarity matrix based on local clique match ing density that is searched by dynamic programming to identify similaritie s in the original structures. The method meets the minimal requirements tha t it works with protein molecules of different sizes and works with gaps an d insertions. Examples are given where similarities between protein structu res have been detected, despite no similarity being detectable by simple in spection.