Conformational entropy in molecular recognition by proteins

By Kendra K. Frederick, Michael S. Marlow, K. Valentine, A. Wand. Nature, 2007

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GEOM: Energy-annotated molecular conformations for property prediction and molecular generation (2020, background): “The affinity is determined by the change in Gibbs free energy of the molecule and protein upon binding, which includes the loss of molecular conformational free energy [82].”
Protein conformational flexibility modulates kinetics and thermodynamics of drug binding (2017, background): “We determined crystal structures of the N-HSP90-L107A mutant in the apo-state and in complexes with representative loop- (1, 6) and helix-binding (14, 16, 20) compounds.”
Dynamic personalities of proteins (2007, background): “Although the free energy of binding is similar for Ca 2p -bound calmodulin interacting with many of these peptide sequences, the enthalpic and entropic contributions vary widely, as measured by isothermal titration calorimetr”
Hierarchical consciousness: the Nested Observer Windows model (2024, background): “Second, proteins receive chemical and electrical signals from their neighbors, e.g. calmodulin (Frederick et al. 2007) and NMDA receptors (Mori and Mishina 1995).”