PocketGraph : graph representation of binding site volumes
- 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.
Author: | Martin Weisel, Jan M. Kriegl, Gisbert SchneiderORCiDGND |
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URN: | urn:nbn:de:hebis:30-66680 |
DOI: | https://doi.org/10.1186/1752-153X-3-S1-P66 |
ISSN: | 1752-153X |
Parent Title (English): | Chemistry central journal |
Publisher: | BioMed Central |
Place of publication: | London |
Document Type: | Article |
Language: | English |
Date of Publication (online): | 2009/08/26 |
Date of first Publication: | 2009/06/05 |
Publishing Institution: | Universitätsbibliothek Johann Christian Senckenberg |
Contributing Corporation: | 4th German Conference on Chemoinformatics Goslar, Germany. 9–11 November 2008 |
Release Date: | 2009/08/26 |
Volume: | 3 |
Issue: | (Suppl 1):P66 |
Page Number: | 1 |
First Page: | 1 |
Last Page: | 1 |
Note: | © 2009 Weisel et al; licensee BioMed Central Ltd. |
Source: | 4th German Conference on Chemoinformatics Goslar, Germany. 9–11 November 2008 ; Chemistry Central Journal 2009, 3(Suppl 1):P66 ; doi:10.1186/1752-153X-3-S1-P66 ; http://www.journal.chemistrycentral.com/content/3/S1/P66 |
HeBIS-PPN: | 215152123 |
Institutes: | Biochemie, Chemie und Pharmazie / Biochemie und Chemie |
Dewey Decimal Classification: | 5 Naturwissenschaften und Mathematik / 54 Chemie / 540 Chemie und zugeordnete Wissenschaften |
Licence (German): | Deutsches Urheberrecht |