Figure 5

Example of prediction: scoring PB combinations. This figure presents the prediction of positions 34 to 43 of cupredoxin amicyanin (Protein DataBank code [41]: 1BXA) with short loops prediction. The true 3D representation is given in (a) with the corresponding amino acid and PB sequences. The prediction gives a probability for every PB at each position. The score (and associated probability) at each position are reported in (b). Only scores more than 1 (superior to random) are indicated. The most probable series of PBs is therefore eojac. The comparison between ehiac from cupredoxin amicyanin and eojac taken from positions 53 to 62 of cyclophilin A (PDB code: 1AWU) gives a root mean square deviation (rmsd) equal to 2.2 Å. From (b) we can compute other high scoring PB series. Two of them are given: ehiac from monoclonal 2E8 FAB antibody (PDB code: 12E8, positions 10–19) and ehjac from Apo intestinal fatty acid-binding protein (PDB code: 1A57, positions 65–74) with associated rmsd of 0.3 Å and 2.5 Å respectively. We used MOLMOL [45] for the image visualizations.