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  • Poster presentation
  • Open Access

PocketGraph: graph representation of binding site volumes

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  • 1 and
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Chemistry Central Journal20093 (Suppl 1) :P66

  • Published:


  • Graph Representation
  • Complex Representation
  • Abstract Description
  • Common Technique
  • Molecular Graph

The representation of small molecules as molecular graphs [1] is a common technique in various fields of cheminformatics. This approach employs abstract descriptions of topology and properties for rapid analyses and comparison. Receptor-based methods in contrast mostly depend on more complex representations impeding simplified analysis and limiting the possibilities of property assignment. In this study we demonstrate that ligand-based methods can be applied to receptor-derived binding site analysis.

We introduce the new method PocketGraph that translates representations of binding site volumes into linear graphs and enables the application of graph-based methods to the world of protein pockets. The method uses the PocketPicker [2] algorithm for characterization of binding site volumes and employs a Growing Neural Gas [3] procedure to derive graph representations of pocket topologies.

Self-organizing map (SOM) projections revealed a limited number of pocket topologies. We argue that there is only a small set of pocket shapes realized in the known ligand-receptor complexes.

Authors’ Affiliations

Johann Wolfgang Goethe-University, Beilstein Endowed Chair for Cheminformatics, Siesmayerstraße 70, D-60323 Frankfurt/Main, Germany


  1. Balaban AT: Applications of Graph Theory in Chemistry. J Chem Inf Comput Sci. 1985, 25: 334-343.View ArticleGoogle Scholar
  2. Weisel M, Proschak E, Schneider G: PocketPicker: Analysis of Ligand Binding-Sites with Shape Descriptors. Chem Cent J. 2007, 1: 7-10.1186/1752-153X-1-7.View ArticleGoogle Scholar
  3. Fritzke B: Growing cell structures – a selforganizing network for unsupervised and supervised learning. Neural Networks. 1994, 7: 1441-1460. 10.1016/0893-6080(94)90091-4.View ArticleGoogle Scholar


© Weisel et al; licensee BioMed Central Ltd. 2009

This article is published under license to BioMed Central Ltd.