The Geometry of Shape Space: Application to Influenza
Shape space was proposed by Perelson and Oster 20 years ago as a conceptual formalism in which to represent antibody/antigen binding. It has since played a key role in computational immunology. Antigens and antibodies are thought of as points in an abstract "shape space" where coordinates of points in this space represent generalized physico-chemical properties associated with various (unspecified) physical properties related to binding, such as geometric shape, hydrophobicity, charge, etc. Distances in shape space between points representing antibodies and (the shape complement of) antigens are assumed to be related to their affinity, with small distances corresponding to high affinity. Up to now, coordinates of points in shape space have been purely implicit.
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