Modifications of the scoring function in FlexX for virtual screening applications

A modification of the hydrogen bond score in the docking program FlexX is p resented. Hydrogen bonds formed in inaccessible regions of protein cavities thereby gain larger weight than others formed at the protein surface. The modified scoring function is tested with thrombin as a target. Secondly, a recently published knowledge-based scoring function is compared to the Flex X scoring function in several database ranking experiments.