CINF 80 |
| Molecular docking is widely used to screen large compound collections for novel lead molecules that complement a receptor of known structure. Docking energy functions are approximate and many degrees of freedom are under-sampled. To understand where algorithms can be improved, we have turned to model systems where predictions can be tested in detail. These are simplified, small buried cavities where the interactions are dominated by one particular term. Thus, the L99A cavity in T4 lysozyme is dominated by non-polar complementarity, the L99A/M102Q cavity has a single hydrogen bond acceptor, and the W191G cavity in cytochrome C peroxidase is dominated by a single ionic interaction. Predicted ligands are being tested for binding, geometry, and protein motion using x-ray crystallography. We use a cycle of theory development and experimental testing in these systems, where mis-predicted ligands and geometries are as informative as correct predictions. |
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Herman Skolnik Award Symposium
2:00 PM-5:50 PM, Tuesday, 12 September 2006 Moscone Center -- Room 122, Oral
Division of Chemical Information |