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Available in Gastown only, everyday until 4pm. Email Address Sign Up. Arm yourself against COVID-19. The global exploration problem is decomposed into a set of separate MD trajectories that can be restarted within a selective process to achieve sufficient phase-space sampling. Accurate statistical properties can be obtained through reweighting. Within this highly parallel setup, the Tinker-HP package can be powered by an arbitrary large number of GPUs on supercomputers, reducing exploration time from years to days.

A detailed clustering analysis exhibits striking differences between FFs, with AMOEBA showing a richer conformational space. Focusing on key structural markers related to sleeping drink oxyanion hole stability, we observe an asymmetry between protomers. Results highlight the plasticity of the Mpro active site. The C-terminal end of its less structured protomer is shown to oscillate between several states, being able to interact with the other protomer, potentially modulating its activity.

Active and distal site volumes are found to be larger in the most active protomer within our AMOEBA simulations compared to non-PFFs as additional cryptic pockets are uncovered. Data show the protonation impact on the destructuring of the oxyanion loop. We finally analyze the solvation patterns around key histidine residues. The confined AMOEBA polarizable water molecules are drunk to explore a wide range of dipole moments, going beyond bulk values, leading to a water molecule count consistent with experimental data.

Results suggest that the use of PFFs could be critical in drug discovery to accurately model the complexity of the molecular interactions structuring Mpro. You can use material from this article in other publications without requesting further permissions from the RSC, provided that the correct acknowledgement is given.

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