Perspectives in Drug Discovery and Design

, Volume 20, Issue 1, pp 231–244 | Cite as

In vitro and in silico affinity fingerprints: Finding similarities beyond structural classes

  • Hans Briem
  • Uta F. Lessel


In this article, we review the use of in vitro and in silico affinity fingerprints as novel descriptors for similarity searches in molecular databases and QSAR analyses. An affinity fingerprint for a particular molecule is constructed as a vector of either its binding affinities, docking scores or superpositioning pseudoenergies against a reference panel of proteins or small molecules. In contrast to most other molecular descriptors, affinity fingerprints are not directly derived from molecular structures. As such, they offer the possibility to detect similarities amongst molecules independent of their structural scaffolds. In this report we introduce the Flexsim-S method, an extension of our previous work on virtual affinity fingerprints. Moreover, we demonstrate that virtual affinity fingerprint methods are comparable to some popular two-dimensional descriptors in terms ofcorrectly classifying compounds, but complementary with respect to the particular search results (hit lists).

affinity fingerprints database searching moleculardescriptors molecular similarity QSAR virtual screening 


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Copyright information

© Kluwer Academic Publishers 2000

Authors and Affiliations

  • Hans Briem
    • 1
  • Uta F. Lessel
    • 1
  1. 1.Department of Lead DiscoveryBoehringer Ingelheim Pharma KGIngelheimGermany

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