A methodology is introduced to assign energy-based scores to two-dimensional (2D) structural features based on three-dimensional (3D) ligand-target interaction information and utilize interaction-annotated features in virtual screening. Database molecules containing such fragments are assigned cumulative scores that serve as a measure of similarity to active reference compounds. The Interaction Annotated Structural Features (IASF) method is applied to mine five high-throughput screening (HTS) data sets and often identifies more hits than conventional fragment-based similarity searching or ligand-protein docking.
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