Three-dimensional pattern matching in protein structure analysis

Many pattern-matching problems that arise in ''one dimension'' in the analysis of genomic sequences have three-dimensional analogs in the analysis of protein structures. This report focuses on the identification and matching of common substructures, and treats two problems: the probing of a database of structures with a segment of a protein to identify regions from other proteins with conformations similar to that of the probe, and the determination of the maximal common ''rigid subunit'' in comparing alternative conformations of a single protein. Approaches based on the representation of structures in terms of lists of coordinates or as a distance matrices are compared.