Structural immunoinformatics

Normal adaptive immune responses operate under major histocompatibility complex (MHC) restriction by binding to specific short antigenic peptides. Sequence-structure-function information is critical in facilitating the understanding of principles governing MHC-specific peptide recognition and binding. Three-dimensional structures of bound peptide ligands to MHC receptors are today characterized in great number using X-ray crystallography, offering a rich source of information for structural analysis. By utilizing information derived from available experimental structures, it is possible to predict binders for alleles that have not been studied extensively and offers an alternative to sequence-based approaches that require a large dataset for training. This chapter will introduce the use of structural descriptors, as well as comparative modeling and docking techniques for predicting whether a peptide sequence can bind to a specific MHC allele.