PEPOP: Computational design of immunogenic peptides

BMC Bioinformatics

Table 3 Reactivity with the cognate Ag of the Abs obtained by immunization with the peptides

¹ Amino acids in lower case are D-amino acids. ² Algorithm used to predict the sequence of the immunogenic peptide: B for BEPITOPE otherwise PEPOP. ³ The reference segment chosen is the longest (L: longest) or the segment at the top (T) of the list of all the segments ranked according to the five characteristics indicated in the text. ⁴ The method of extension chosen is either elongation with the flanking protein sequence (FPS); addition of the nearest neighbor (NN) segment(s) regardless of the sense of the segment added: if the segment is in the unnatural sense, i.e., from the C-terminus to the N-terminus, it is synthesized using D-amino acids (NNd); or manual design (MD). ⁵ The area of extension is the cluster top of the list (TC: top cluster) of the clusters ranked according to the five characteristics (see the text), or the cluster containing the selected reference segment (CC: containing cluster), or a user selected cluster (SC: selected cluster), or none when the reference segment is the longest and the method is the FPS. ⁶ Positive reactivities in the indirect ELISA are values over 0.2, and strong reactivities are values over 1.0. Control experiments done by using the preimmune serum gave values ranging from 0.0020 to 0.0028. The given values correspond to specific absorbances (A450 nm immune serum – A450 nm preimmune serum).

ISSN: 1471-2105