Identifying vaccine escape sites via statistical comparisons of short-term molecular dynamics.

ABSTRACT: The identification of viral mutations that confer escape from antibodies is crucial for understanding the interplay between immunity and viral evolution. We describe a molecular dynamics (MD)-based approach that goes beyond contact mapping, scales well to a desktop computer with a modern graphics processor, and enables the user to identify functional protein sites that are prone to vaccine escape in a viral antigen. We first implement our MD pipeline to employ site-wise calculation of Kullback-Leibler divergence in atom fluctuation over replicate sets of short-term MD production runs thus enabling a statistical comparison of the rapid motion of influenza hemagglutinin (HA) in both the presence and absence of three well-known neutralizing antibodies. Using this simple comparative method app

SUBMITTER: Rajendran M 

PROVIDER: S-EPMC8978532 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature