Designing antibodies that bind specific epitopes and epitopes that avoid specific antibodies

Biological processes are mediated by specific interactions of proteins. Hence, designing proteins that specifically recognize, or specifically avoid, a given epitope may allow control and manipulation of biological process. We developed a computer guided approach for the design of epitope specific binding. Using this approach, we design proteins that specifically recognize a given site on another protein. A similar approach allows the design of epitope specific avoidance. That is, we can use it to design proteins that avoid binding of a given element in other proteins. We show how the design of epitope specific binding can be implemented to create therapeutic antibodies with a predefined mechanism of action, such as agonism or antagonism. We also show epitope specific avoidance can be used to design safe compounds that avoid interactions with the immune system in the context of allergy and food sensitivities.