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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