For every candidate loop obtained and explored in the previous steps of the pipeline, the user needs to identify its corresponding insert loop needs to be identified. In this step, the loops are either paired automatically or manually by the user. If the automatic process was selected, the experts now need to verify the suitability of the loop pairing, for the posterior grafting. This is achieved, similarly as in the step three, by comparing their geometrical properties to the individual loops. The process assumes a certain amount of structural similarity in between the scaffold and the insert proteins. Thus, only loops in equivalent structural regions should be paired. Although very different pairs of loops may be chosen for grafting here (i.e different geometries or pairs of loops from different structural regions), this is extremely discouraged. Furthermore, pairing loops from different structural regions will not produce any results.