Absolute Binding Free Energy Calculations Bovine Pancreas Beta-Trypsin in Complex with Benzamidine
Lau, Stephen; Jean, Bernandie; Madura, Jeffry
Department of Chemistry and Biochemistry
Knowing the binding free energy between a protein and a small molecule is an important quantity in the drug discovery process. CHARMM-GUI Ligand Binder allows users to calculate the absolute binding free energy of a small molecule bound to a protein using the free energy perturbation/molecular dynamics (FEP/MD) techniques. The CHARMM-GUI will be used to calculate the binding free energy between the protein trypsin and two substrates, benzamidine and para-fluorobenzamidine. This protein substrate system is used to validate the CHARMM-GUI interface.