An imbalance in the gut microbiome is linked to immune disorders, such as autoimmune, allergic, and chronic inflammatory disorders. Elucidation of disease mechanisms is a matter of urgency. It requires precise elucidation of the structure-based mechanisms of protein interactions involved in disease onset. In addition, an understanding of the protein dynamics is vital because these fluctuations affect the function and interaction of disease-associated proteins. Experimental evaluation of not only protein interactions, functions, and structures but also the dynamics are time-consuming; therefore, computational predictions are necessary to elucidate disease mechanisms. Here, we introduce recent studies on structure-based analyses of proteins using computational approaches, particularly artificial intelligence (AI) and molecular dynamics (MD) simulations.
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