Chapter 9 Calculating Binding Free Energy in Protein–Ligand Interaction

摘要: Publisher Summary This chapter examines the calculation of binding free energy in protein–ligand interaction. A deeper understanding way a protein recognizes its biologically relevant ligand or small molecule inhibitor will have profound effect on biological recognition processes and ability to design therapeutics. Binding affinity can be estimated experimentally by kinetic experiments that measure inhibition enzyme presence both substrate is reported as an constant. Theoretical calculations determine more direct fashion calculating properties individual structures protein, ligand, complex, their ensembles. state function treated such these calculations, which means it independent path taken from reactants product. Polarization charge transfer play significant role molecular interactions. Such effects captured using quantum mechanics. Rigorous exhaustive electrostatic interaction energies performed at high levels theory. are feasible only for model chemistries severely restricted computational cost associated with study larger molecules.