OptiMatrix
Once a T cell epitope cluster has been identified, it may be necessary to devise a strategy for binding optimization by improving the “agretope” (i.e. the interface with an HLA molecule). The OptiMatrix algorithm simplifies this process by identifying those individual amino acids that contribute the least to binding affinity across both peptide frames and HLA alleles. Changes in these “sensitive” amino acids can have a disproportional impact on the immunogenicity of the underlying sequence. Once a set of target amino acids, and their respective pocket positions within the peptide, have been identified, an additional set of viable replacement amino acids can be developed. This can be accomplished in two ways; by either looking at the Blast Summary report to identify changes already existing and tolerated in other species or variants of the target protein or by developing a 3D model of the target protein and screening a set of immunogenic changes for low impact alternatives. These identified replacement amino acids (from conservative changes or complex changes) can then be inserted back into the original peptide sequence. The disproportional impact on immunogenicity can then be seen in real-time as you substitute one original residue with its respective replacement. The sequences optimized for binding, as suggested by OptiMatrix (originals plus modifications), can then be validated in-vitro (see below) before being tested for functionality.
