IS-score is a tool for evaluating the quality of structural models of protein-protein complexes. One can perform pairwise comparison (i.e, model vs target structure), or compare a set of models against their corresponding target structure, which is usually a crystal structure from an experimental study. Two metrics, the Interface Similarity score (IS-score) and the interfacial Template Modeling score (iTM-score), are implemented to evaluate the interface similarity between a docking model and its target. Note that the IS-score evaluation requires a sequence correspondence between the model and the target structure. Usually the two structures have identical sequences, though gaps are allowed. If you want to compare complex structures without predefined sequence correspondence, consider iAlign, which returns an optimal interface alignment using the complex structures. Details of the IS-score program can be found in the following references:
Mu Gao and Jeffrey Skolnick, 2011, New benchmark metrics for protein-protein docking methods. Proteins. Proteins: Structure, Function, and Bioinformatics. 79(5):1623-1634. PDF