Computational Methods in Immunology and Vaccinology: Design and Development of Antibodies and Immunogens

The design of newbiomolecules able to harness immunemechanismsfor the treatment of diseases is a prime challenge for computationaland simulative approaches. For instance, in recent years, antibodieshave emerged as an important class of therapeutics against a spectrumof pathologies. In cancer, immune-inspired approaches are witnessinga surge thanks to a better understanding of tumor-associated antigensand the mechanisms of their engagement or evasion from the human immunesystem. Here, we provide a summary of the main state-of-the-art computationalapproaches that are used to design antibodies and antigens, and inparallel, we review key methodologies for epitope identification forboth B- and T-cell mediated responses. A special focus is devotedto the description of structure- and physics-based models, privilegedover purely sequence-based approaches. We discuss the implicationsof novel methods in engineering biomolecules with tailored immunologicalproperties for possible therapeutic uses. Finally, we highlight theextraordinary challenges and opportunities presented by the possibleintegration of structure- and physics-based methods with emergingArtificial Intelligence technologies for the prediction and designof novel antigens, epitopes, and antibodies.