Abstract
BackgroundBioinformatics methods are helpful to identify new molecules for diagnostic or therapeutic applications. For example, the use of peptides capable of mimicking binding sites has several benefits in replacing a protein which is difficult to produce, or toxic. Using peptides is less expensive. Peptides are easier to manipulate, and can be used as drugs. Continuous epitopes predicted by bioinformatics tools are commonly used and these sequential epitopes are used as is in further experiments. Numerous discontinuous epitope predictors have been developed but only two bioinformatics tools have been proposed so far to predict peptide sequences: Superficial and PEPOP 2.0. PEPOP 2.0 can generate series of peptide sequences that can replace continuous or discontinuous epitopes in their interaction with their cognate antibody.ResultsWe have developed an improved version of PEPOP (PEPOP 2.0) dedicated to answer to experimentalists’ need for a tool able to handle proteins and to turn them into peptides. The PEPOP 2.0 web site has been reorganized by peptide prediction category and is therefore better formulated to experimental designs. Since the first version of PEPOP, 32 new methods of peptide design were developed. In total, PEPOP 2.0 proposes 35 methods in which 34 deal specifically with discontinuous epitopes, the most represented epitope type in nature.ConclusionThrough the presentation of its user-friendly, well-structured new web site conceived in close proximity to experimentalists, we report original methods that show how PEPOP 2.0 can assist biologists in dealing with discontinuous epitopes.
Highlights
Bioinformatics methods are helpful to identify new molecules for diagnostic or therapeutic applications
The web interface is composed of 3 sections that can correspond to different ways to use PEPOP 2.0 in experimental projects
Because we predict from the native Ag, we showed that only a limited number of peptides is necessary to map discontinuous epitopes
Summary
Bioinformatics methods are helpful to identify new molecules for diagnostic or therapeutic applications. Continuous epitopes predicted by bioinformatics tools are commonly used and these sequential epitopes are used as is in further experiments. Numerous discontinuous epitope predictors have been developed but only two bioinformatics tools have been proposed so far to predict peptide sequences: Superficial and PEPOP 2.0. PEPOP 2.0 can generate series of peptide sequences that can replace continuous or discontinuous epitopes in their interaction with their cognate antibody. The antigen-antibody (Ag-Ab) interaction is the basis of the immune system, and the Ab is a valuable tool in various biomedical applications, including diagnosis and therapy research [1, 2]. Immunogenicity is the ability of a molecule to induce an immune response in the host, yielding Abs. Antigenicity is the ability of a molecule to bind to an Ab. Abs are known to exhibit highly specific binding, though off-target binding can occur [3].
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