Principal Investigator: Prof. Giri Narasimhan
Principal Architect: Vitalii Stebliankin
Other Contributors: Prabin Baral, Christian Balbin, Janelle Nunez-Castilla, Masrur Sobhan, Trevor Cickovski, Ananda Mohan Mondal, Jessica Siltberg-Liberles, Prem Chapagain, Kalai Mathee

Epitope-based molecular mimicry occurs when an antibody cross-reacts with two different antigens due to structural and chemical similarities. Molecular mimicry between proteins from two viruses can lead to beneficial cross-protection when the antibodies produced by exposure to one also react with the other. On the other hand, mimicry between a protein from a pathogen and a human protein can lead to auto-immune disorders if the antibodies resulting from exposure to the virus end up interacting with host proteins. While cross-protection can suggest the possible reuse of vaccines developed for other pathogens, cross-reaction with host proteins may explain side effects. We present a comprehensive Epitope-based Molecular Mimicry Search (EMoMiS) pipeline for computational molecular mimicry searches. As a first step, antigens extracted from the Structural Antibody Database (SAbDab) are searched for sequence regions and structural similarity with the target protein. Then, a pre-trained deep learning model is used to evaluate if antibodies, known to recognize the SAbDab antigens, can cross-react with the target structure. The developed pipeline is generic and can be applied to find mimicry for novel pathogens.

Download Github Site: EMoMiS
Contact: Prof. Giri Narasimhan

Stebliankin, Baral, Nunez-Castilla, Sobhan, Cickovski, Mondal, Siltberg-Liberles, Chapagain, Mathee, and Narasimhan. A Pipeline for Epitope-based Molecular Mimicry Search in Protein Structures with Applications to SARS-CoV-2 (Under Review, 2022)