For every candidate loop obtained and explored in the previous steps of the pipeline, the user needs to identify its corresponding insert loop. In this step, the loops are paired manually by the user. The pairing is largely a mechanical process, however, the experts now need to verify the suitability of the additional loops, added in the Steps 3 and 4, for the grafting. This is achieved, similarly as in the step one, 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. not from the same structural regions), this is discouraged and will only result in the lack of production of results (see next step).