A Ligand That Is Predicted to Bind Better to Avidin than Biotin: Insights from Computational Fluorine Scanning

By Bernd Kuhn and, Peter A. Kollman. 2000

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Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions. (2001, methodology): “Another application of this MM/PBSA method to study biotin and its derivatives binding with avidin/streptavidin was carried out by Kuhn & Kollman (82).”
Approaches to efficiently estimate solvation and explicit water energetics in ligand binding: the use of WaterMap (2013, unknown): “Solvation models, that is, theoretical treatments that describe the effect of solvent range from continuum (implicit) solvent models [20-27] to explicit solvent models [28-31] and in the most sophisticated cases a quantum mechanical treatment [15,32,33] (not discussed in this article).”
Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. (2003, methodology): “The related MMPoisson–Boltzmann (PB) SA approach has been applied to compare relative stabilities of different conformations of nucleic acids,(55) to identify correctly folded proteins,(56) and to estimate binding affinities of small molecules binding to proteins.(57) – 59 It has been used to predic”