Allosteric drugs are commonly explained with structures: a ligand occupies a distal pocket, the protein adopts a different conformation, and activity changes at a functional site. Molecular dynamics (MD) complicates this account because it can reveal state populations, transient pockets, coupled fluctuations and communication routes that are absent from endpoint structures. Yet the appearance of motion in a trajectory does not itself establish a new mechanism. This Perspective asks a narrower question: when does MD change mechanistic interpretation rather than merely enrich structural description? Across recent examples, mechanistic reinterpretation becomes plausible when simulation changes an inference about which states are populated, how transitions occur, how distant regions become coupled, or why different ligands produce different functional consequences. The same evidence also exposes important limits. Communication networks depend on representation, transient states can be undersampled, pathway reconstructions can be method-sensitive, and single long trajectories can give a misleading impression of convergence. We therefore distinguish dynamic observation from mechanistic attribution and treat experimental concordance, sampling reproducibility and analysis robustness as constraints on interpretation. This approach positions MD not as an automatic mechanism generator, but as an inference-changing tool whose mechanistic weight depends on what it alters in the explanatory model and how well that alteration survives competing computational and experimental accounts.
IJPRAS
