PEPOP. (A) Description of PEPOP. Step 1: The solvent accessible surface area is calculated from the 3D structure of a protein. Step 2: Segments of accessible and contiguous amino acids are listed, and the shortest Euclidian distance matrix between segments is calculated. Step 3: The segments are clustered according to the matrix (clusters can be displayed on the 3D structure of the Ag). Step 4: Peptides are designed according to the clustering analyses. (B) The PEPOP interface. Segments and clusters can interactively be displayed on a 3D view of the Ag.