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Allen, P., Nguyen, N., Humphrey, N.D., Mao, J., Chavez-Bonilla, D. and Sorin, E.J. (2024) A Hands-On Collaboration-Ready Single- or Interdisciplinary Computational Exercise in Molecular Recognition and Drug Design. Education Sciences, 14, Article No. 139. https://doi.org/10.3390/educsci14020139

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• TITLE: On Docking and Binding

  AUTHORS: Yi Fang

  KEYWORDS: Docking, Binding, Conformational Gibbs Free Energy Function, Post-Binding Reshaping, Binding Affinity, Hydrophobic, Hydrophilic

  JOURNAL NAME: Journal of Biosciences and Medicines, Vol.14 No.6, June 30, 2026

  ABSTRACT: The single molecule conformational Gibbs free energy function (CGF) is rigorously derived via quantum statistics. Apply it as scoring function in docking we obtain analytic docking Gibbs free energy formula. Line by line estimates of the formula establishes the necessary and sufficient conditions to make the docking Gibbs free energy as negative as possible. These conditions form the binding pose searching strategy: the binding sites, pieces on surfaces of receptor and ligand, must be close enough, both geometrically and electronically complementary. Electronically complementary has two cases: either both binding sites are large hydrophobic pieces with smaller hydrophilic pieces or large hydrophilic pieces with smaller hydrophobic pieces. A single molecule theory of molecular folding based on CGF and single molecule thermodynamic hypothesis (SMTH) reveals that non-covalent and covalent binding will induce folding and conformational change, called post-binding reshaping. Applying this theory we resolve all three major unresolved problems in docking posted in 2017, 1. Tackling binding site flexibility; 2. Treating solvent during docking; 3. Affinity prediction in docking. Especially post-binding reshaping resolves the mystery of significant conformational change on covalent binding.