TY  - JOUR
A1  - Weisel, Martin
A1  - Kriegl, Jan M.
A1  - Schneider, Gisbert
T1  - PocketGraph : graph representation of binding site volumes
T2  - Chemistry central journal
N2  - 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.
Y1  - 2009
UR  - http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/6785
UR  - https://nbn-resolving.org/urn:nbn:de:hebis:30-66680
SN  - 1752-153X
N1  - © 2009 Weisel et al; licensee BioMed Central Ltd.
VL  - 3
IS  - (Suppl 1):P66
SP  - 1
EP  - 1
PB  - BioMed Central
CY  - London
ER  -