Fig. 1

PEPOP 2.0 web-site. The first result page of PEPOP 2.0, after the user gives the 3D structure of the protein, proposes 3 different ways to design peptides. a The ‘One Specific Peptide Design’ predicts one peptide at a time through 5 steps where the user has to select the reference segment (first insert), the method of extension, the area of extension and the peptide length; the fifth step (second insert) gives the peptide sequence and displays it on the 3D structure of the protein. b To design peptides in the ‘Paired Peptide Design’ section, the user selects the method of extension, the peptide length and eventually the aa from which the first pair has to be determined (first insert); the 5 peptide pairs are summarized in one side of the browser and displayed on the 3D structure of the protein on the other side of the browser. c In the ‘Peptide Bank Design’, the user has to select the method(s) and the peptide length (first insert); all the predicted peptides can be displayed on the 3D structure of the protein (second insert)