Journal of Computer-Aided Molecular Design

, Volume 20, Issue 12, pp 703–715 | Cite as

High-throughput structure-based pharmacophore modelling as a basis for successful parallel virtual screening

  • Theodora M. Steindl
  • Daniela Schuster
  • Gerhard Wolber
  • Christian Laggner
  • Thierry LangerEmail author
Original Paper


In order to assess bioactivity profiles for small organic molecules we propose to use parallel pharmacophore-based virtual screening. Our aim is to provide a fast, reliable and scalable system that allows for rapid in silico activity profile prediction of virtual molecules. In this proof of principle study, carried out with the new structure-based pharmacophore modelling tool LigandScout and the high-performance database mining platform Catalyst, we present a model work for the application of parallel pharmacophore-based virtual screening on a set of 50 structure-based pharmacophore models built for various viral targets and 100 antiviral compounds. The latter were screened against all pharmacophore models in order to determine if their known biological targets could be correctly predicted via an enrichment of corresponding pharmacophores matching these ligands. The results demonstrate that the desired enrichment, i.e. a successful activity profiling, was achieved for approximately 90% of all input molecules. Additionally, we discuss descriptors for output validation, as well as various aspects influencing the analysis of the obtained activity profiles, and the effect of the searching mode utilized for screening. The results of the study presented here clearly indicate that pharmacophore-based parallel screening comprises a reliable in silico method to predict the potential biological activities of a compound or a compound library by screening it against a series of pharmacophore queries.


Bioactivity profiling Virtual screening Pharmacophore modelling LigandScout Structure-based pharmacophores Database mining Parallel screening 


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Copyright information

© Springer Science+Business Media B.V. 2006

Authors and Affiliations

  • Theodora M. Steindl
    • 1
  • Daniela Schuster
    • 2
  • Gerhard Wolber
    • 1
  • Christian Laggner
    • 2
  • Thierry Langer
    • 1
    • 2
    Email author
  1. 1.Inte:Ligand GmbHMaria EnzersdorfAustria
  2. 2.Institute of Pharmacy, Computer Aided Molecular Design Group, and Centre of Molecular BiosciencesUniversity of InnsbruckInnsbruckAustria

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