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  • Title: Three-dimensional protein-ligand interaction scaling of two-dimensional fingerprints.
    Author: Tan L, Vogt M, Bajorath J.
    Journal: Chem Biol Drug Des; 2009 Nov; 74(5):449-56. PubMed ID: 19793181.
    Abstract:
    We introduce a computational scaling methodology that utilizes protein-ligand interaction information extracted from complex crystal structures to enrich similarity searching using structural fingerprints with compound class-specific information. Scaling factors are derived to emphasize fingerprint bit positions that result from interacting fragments of bound ligands and correspond to frequently occurring structural features. Through interaction-based scaling, this information is transferred to standard fingerprints of multiple reference compounds. In systematic search calculations, fingerprints scaled on the basis of three-dimensional information are found to produce higher recall rates of active compounds than alternative types of scaled and non-scaled fingerprints.
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