Background:
Phage display is a powerful and versatile technology for the identification
of peptide ligands binding to multiple targets, which has been successfully employed in
various fields, such as diagnostics and therapeutics, drug-delivery and material science. The
integration of next generation sequencing technology with phage display makes this methodology
more productive. With the widespread use of this technique and the fast accumulation
of phage display data, databases for these data and computational methods have become an
indispensable part in this community. This review aims to summarize and discuss recent progress
in the development and application of computational methods in the field of phage display.
Methods:
We undertook a comprehensive search of bioinformatics resources and computational
methods for phage display data via Google Scholar and PubMed. The methods and
tools were further divided into different categories according to their uses.
Results:
We described seven special or relevant databases for phage display data, which provided
an evidence-based source for phage display researchers to clean their biopanning results.
These databases can identify and report possible target-unrelated peptides (TUPs),
thereby excluding false-positive data from peptides obtained from phage display screening
experiments. More than 20 computational methods for analyzing biopanning data were also
reviewed. These methods were classified into computational methods for reporting TUPs, for
predicting epitopes and for analyzing next generation phage display data.
Conclusion:
The current bioinformatics archives, methods and tools reviewed here have
benefitted the biopanning community. To develop better or new computational tools, some
promising directions are also discussed.
Selection of peptide ligands for the antimucin core antibody C595 using phage display technology: definition of candidate epitopes for a cancer vaccine