COMP 400 |
| Crystal structures provide one view of the water structure around a protein surface. The information content from a crystal structure is typically insufficient to be able to differentiate between tightly bound water molecules and those less tightly bound yet still present in the crystal structure. An understanding of this binding differential is essential when doing structure based drug design. A novel approach has been developed which permits the calculation of binding free energies of fragments against a protein using a series of Grand Canonical Monte Carlo simulations. Through a process of simulated annealing of chemical potential we obtain accurate binding energies for fragments interacting with a protein. We also obtain exceptional information about the binding of water to the protein surface. This information enables us to explicitly identify binding sites for proteins and design high affinity, selective molecules. A cancer target of interest in the pharmaceutical industry, HSP-90, will be used as a demonstration of how this information has been applied to further our understanding of how to use water structure in fragment centered structure based drug design |
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Free Energy Computations in Drug Discovery
1:00 PM-6:00 PM, Thursday, 14 September 2006 Moscone Center -- Room 220/222, Oral
Division of Computers in Chemistry |