Background: Selective Cationic Amphipathic Antibacterial Peptides (SCAAPs) occupy a prominent place in the
production of new drugs on account of their high toxicity towards bacteria and low toxicity towards mammalian cells, low
hemolytic activity, and contribution to the protection of the human immune system.
Introduction: Their number in nature is very low and experimental tests are very protracted and costly. Therefore, it would
be useful to have bioinformatics tools that would identify them in the existing databases and also propose new synthetic
Method: In order to reduce the costs of identification and/or chemical synthesis. To know the physicochemical characteristics of SCAAPs at a residues level and to obtain a “bioiformatics fingerprint” suitable for their selection, we have modified
the Polarity Index Method® (PIM®) to include the α-helical configuration of each sequence to determine their individual
“PIM® profile”. We have also used a set of computer program to determine their “Intrinsic Disorder Predisposition”. This
information was then compared with other protein groups such as bacteria, fungi, virus and cell penetrating peptides (CPP)
from the UniProt database and a set of intrinsically disordered proteins. Once the “fingerprint” of SCAAPs was obtained, it
was used for searching among the 559228 “reviewed” proteins from the UniProt database and a set of synthetic SCAAPs
characterized by the predefined “PIM® profile” selected.
Results: Our results showed that the metric named “PIM® profile” can identify, with a high level of accuracy, a group of
bacterial SCAAPs. This bioinformatics study was supported at residues level, using the in-house bioinformatics system
Polarity Index Method the commonly used algorithm for the prediction of intrinsic disorder predisposition, PONDR®
Conclusions: The Polarity Index Method seems highly efficient identifying SCAAP candidates.