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  • Poster presentation
  • Open Access

Mining public-source databases for structure-activity relationships

  • 1,
  • 2 and
  • 2
Journal of Cheminformatics20102 (Suppl 1) :P4

  • Published:


  • Enrichment Analysis
  • Structural Detail
  • Public Information
  • Activity Information
  • Reported Activity

Modeling off-target effects has become a highly important and relevant component of the computational chemistry toolset. The presentation will describe a new contribution that seeks to allow the extraction of 3D-structure-activity relationships from public information starting from a chemical structure. Several public source databases such as PubChem [1] offering structure as well as activity information for a number of targets have been examined for their value in extracting useful structure-activity relationships (SARs). A Topomer search [2] of public-source databases using the structures of a set of 255 marketed drugs [3] as queries yielded sets of shape- and pharmacophore similar hits. SAR-tables were constructed by collecting hits around each query structure and for a particular reported activity. A new method: quantitative series enrichment analysis (QSEA) [4] was applied to these SAR-tables to capture trends and to transform these trends into 3D-QSAR models. Overall more than 400 SAR-tables with Topomer CoMFA models were found by extracting trends from the PubChem and ChemBank [5] database. The resulting models were able to highlight the structural details of certain off-target effects of marketed drugs even in those cases where the traditional structural similarity would conclude that no off-target effect would exist. This demonstrates the usefulness of the approach in modeling off-target effects.

Authors’ Affiliations

Elara Pharmaceuticals, Heidelberg, Germany
Tripos International, Martin-Kollar-Str. 17, München, Germany


  1. []
  2. Cramer RD: J Chem Inf Comp Sci. 2004, 44: 1221-1227.View ArticleGoogle Scholar
  3. Cleves AE, Jain AN: J Med Chem. 2006, 49: 2921-2938. 10.1021/jm051139t.View ArticleGoogle Scholar
  4. Wendt B, Cramer RD: J Comp Aided Mol Des. 2008, 22: 541-555. 10.1007/s10822-008-9195-6.View ArticleGoogle Scholar
  5. []


© Bernd et al; licensee BioMed Central Ltd. 2010

This article is published under license to BioMed Central Ltd.