Protein libraries provide a way to probe and identify new amino acid sequences of interest. A library ofprotein sequences can be created by randomizing certain amino acids, while maintaining specificresidues in strategic positions. These libraries can then be screened and sorted according to theircharacteristics. In this seminar, two protein libraries are going to be discussed: (1) the epitope libraryand (2) the adeno associated virus (AAV) library.

Epitopes are small protein regions in antigens recognized by antibodies. Predicting which antigenicsequences will bind to specific antibodies is a challenging yet an essential task for developing newvaccines and in vitro antibody testing. By creating epitope libraries one can understand and predictthese recognition patterns. In this project we explore the use of microfluidics as a high-throughputmethod for screening and selection of a created epitope library.

AAV are virus with great promise for gene therapy, since they lack pathogenicity, infect non-dividingcells and can integrate well into the host genome. The goal of creating a AAV library is to increase thetropism of this virus, that is its ability to infect tissues. VP3 is the protein of AVV that contains allsurface-exposed residues of the viral capsid that contribute to its tropism. In this project, werandomized the variable regions of the VP3 sequence, through quantum algorithms and by taking intoconsideration insights from computational protein design.

The methods developed in these projects can be applied for numerous types of protein libraries,demonstrating the importance of these libraries as tools in protein engineering, understanding protein-protein interaction and ultimately in the development of new therapeutics.