Which metric derived from MD simulations offers a quantitative measure of binding strength that directly correlates with a drug's effectiveness at lower concentrations?
Answer
Binding free energy
Binding free energy is a critical thermodynamic calculation performed using advanced MD methods, such as free energy perturbation or thermodynamic integration. This calculation provides a physically grounded quantification of the strength of the interaction between the drug candidate and its target protein under actual physiological conditions. A lower, more favorable binding free energy indicates a stronger association, meaning the drug will remain bound longer and be more effective, especially at lower concentrations, making this metric superior to simple scoring functions provided by standard docking programs.
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