CINF 79 |
| Even after more than a decade of research, molecular docking remains a challenging task. The scoring problem and the proper handling of protein flexibility aside, also other issues are still largely unresolved. We enhanced the docking software FlexX in several ways to challenge some of these. First of all, we added functionality to provide a more appropriate treatment of water molecules in the active site. Secondly, we introduced a new way of handling metal ions explicitly considering the different possible coordination geometries. Third, we implemented a completely novel placement strategy (single interaction scan) that has proven to be most suitable especially in cases of largely hydrophobic active sites. Finally, we took measures to be able to combine the new modules among each other as well as with the established extensions for handling of pharmacophore constraints, combinatorial library docking and the simultaneous consideration of multiple active site conformations. All together this provides a powerful set of tools rise to the the challenge of molecular docking. We provide recent results using this functionality in a series of application examples. |
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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 |