High-Throughput Molecular Dynamics-Based Alchemical Free Energy Calculations for Predicting the Binding Free Energy Change Associated with the Selected Omicron Mutations in the Spike Receptor-Binding Domain of SARS-CoV-2.

Biomedicines · 2022 · PMC9687918 · PMID 36359299

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fairly significantno p-value reported

Since the conformational changes at the protein–protein binding interfaces can be fairly significant the longer the MD-simulation lasts, we investigated the effect of the length of the simulation on the Prime/MM-GBSA energy values.

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