2024
DOI: 10.1021/acs.jcim.4c01361
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Comparative Assessment of Water Models in Protein–Glycan Interaction: Insights from Alchemical Free Energy Calculations and Molecular Dynamics Simulations

Deng Li,
Mona S. Minkara

Abstract: Accurate computational simulations of protein− glycan dynamics are crucial for a comprehensive understanding of critical biological mechanisms, including host−pathogen interactions, immune system defenses, and intercellular communication. The accuracy of these simulations, including molecular dynamics (MD) simulation and alchemical free energy calculations, critically relies on the appropriate parameters, including the water model, because of the extensive hydrogen bonding with glycan hydroxyl groups. However,… Show more

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