Faculty of Engineering and Natural Sciences
Accurate Calculation of Binding Free Energies from Umbrella Sampling Potential of Mean Force Calculations
Serdar Kuyucak, METU, Ankara
Binding constants and binding free energies are the most important quantities that characterize the protein-ligand interactions. in recent years, there has been steady progress in calculation of these quantities from molecular dynamics simulations, and the desired aim of "chemical accuracy" has been achieved for some small ligands. In this talk an overview of various methods used in free energy calculations will be given, and the umbrella sampling method--which is expected to work best for large ligands--will be applied to a potassium ion channel-toxin complex. It will be shown that accurate binding free energies of a ligand peptide can be obtained once the distortion of the peptide is prevented using appropriate restraints.
Prof. Kuyucak graduated from Middle Technical University Physics Department ( B.Sc.) and Yale Univeristy Physics Department ( 1982). He worked on Nuclear Physics in Germany and Australia for for 20 years. He has been working at Sydney Univeristy Physics department since 2003 working on several biophyics problems involving Molecular Dynamics studies.
October 6, 2010, 13:40, FENS G032