Uncovering the underlying physical mechanisms of biological systems via quantification of landscape and flux

Xu Li^{1, †,}, Chu Xiakun¹, Yan Zhiqiang¹, Zheng Xiliang¹, Zhang Kun¹, Zhang Feng¹, Yan Han¹, Wu Wei¹, Wang Jin^{1, 2, ‡,}

Funneled energy landscape and energy spectrum of ligand binding. (a) Diverse docking conformations of the target COX-2 with a drug SC-558, the native binding pose (sticks in red); other decoys (lines in blue). (b) The energy spectrum for decoy ensemble. (c) The resultant binding energy distribution, where ΔEis the variance of energy, 〈E_D〉 is the average of energy of decoy ensemble, and δEis the energy gap. (d) Binding energy landscape with a funnel shape pointing to the native state.^[36]