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PocketGraph: graph representation of binding site volumes
Chemistry Central Journal volume 3, Article number: P66 (2009)
The representation of small molecules as molecular graphs  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  algorithm for characterization of binding site volumes and employs a Growing Neural Gas  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.
Balaban AT: Applications of Graph Theory in Chemistry. J Chem Inf Comput Sci. 1985, 25: 334-343.
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.
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.
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Weisel, M., Kriegl, J. & Schneider, G. PocketGraph: graph representation of binding site volumes. Chemistry Central Journal 3, P66 (2009). https://doi.org/10.1186/1752-153X-3-S1-P66
- Graph Representation
- Complex Representation
- Abstract Description
- Common Technique
- Molecular Graph