Wednesday, July 9, 2014

Abstract-Stephen Lau

Absolute Binding Free Energy Calculations Bovine Pancreas Beta-Trypsin in Complex with Benzamidine
Lau, Stephen; Jean, Bernandie; Madura, Jeffry
Department of Chemistry and Biochemistry
Duquesne University

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.

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