1. A computer-implemented method of generating a local-global alignment score that indicates a global and a local similarity between a first protein structure and a second protein structure, the method executed by a computer system and comprising: receiving, at the computer system, a protein structure correspondence having a plurality of positions indicating a corresponding pair of residues in the first protein structure and the second protein structure; determining, by the computer system and according to a plurality of specified threshold values, a plurality of root mean square deviations corresponding to a plurality of sets of pairs of residues, each set including a plurality of pairs of residues that are contiguous in the protein structure correspondences; selecting, by the computer system, a longest contiguous segment corresponding to a set of pairs of residues of the plurality of pairs of residues based on the plurality of root mean square deviations; determining, by the computer system, a global distance test value based on a plurality of distance scores, each score corresponding to a number of pairs of residues in the correspondence within a pre-defined distance of a plurality of pre-defined distances; generating, by the computer system, the local-global alignment score based on the longest contiguous segment and the global distance test value; and providing, by the computer system, a result based on the local-global alignment score.