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Decoding the Physical Mechanisms of Protein-Small Molecule Association by Multiscale Kinetic Monte-Carlo Simulations

Protein-small molecule association involves multiple recognition stages governed by distinct physical interactions, yet resolving their kinetic contributions remains computationally challenging. Here, we develop a multiscale Monte Carlo framework that combines an atomistic, conformationally flexible ligand with a coarse-grained protein binding pocket and an atomistic steric envelope. Association…

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