The schematic representation of how to create a non-sequential test sets. (1) One protein structure to be permuted is randomly chosen from each target pair. Original residue numbers are indicated inside circles. The three SSEs (strands) are represented by arrows. (2) The original chain is splitted into several segments at loop positions. In this example, the chain has been divided into three segments A, B and C. (3) The segment order is randomly shuffled (e.g. the order A-B-C was shuffled into different order B-C-A). Residue numbers are reassigned according to the shuffled segment order. (4) The generated structure by the permutation technique. Its residue numbers are also modified according to the segment order. The reference alignment are modified according to the reassigned residue numbers of the permuted protein. A’, B’ and C’ represent segments of the other protein structure which has not been chosen for sequence shuffling. Segments A’, B’ and C’ correspond structurally to segments A, B and C respectively.