Epitopedia: identifying molecular mimicry of known immune epitopes

Motivation Upon infection, pathogen epitopes stimulate the host’s immune system to produce antibodies targeting the pathogen. Molecular mimicry (structural similarity) between an infecting pathogen and host proteins or pathogenic proteins the host has previously encountered can impact the immune response of the host. The ability to identify potential molecular mimicry for a pathogen can illuminate immune effects with importance to pathogen treatment and vaccine design. Summary Epitopedia allows for identification of regions with three-dimensional molecular mimicry between a protein in a pathogen with known epitopes in the host. Results SARS-CoV-2 Spike returns molecular mimicry with 14 different epitopes including integrin beta-1 from Homo sapiens , lethal factor precursor from Bacillus anthracis , and pollen allergen Phl p 2 from Timothy grass. Availability Epitopedia is primarily written in Python and relies on established software and databases. Epitopedia is available at under the opensource MIT license and is also packaged as a docker container at . Contact cbalbin{at}fiu.edu, jliberle{at}fiu.edu ### Competing Interest Statement The authors have declared no competing interest.