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Open Access Highly Accessed Research article

Prediction of protein-binding areas by small-world residue networks and application to docking

Carles Pons12, Fabian Glaser3* and Juan Fernandez-Recio1*

Author Affiliations

1 Joint BSC-IRB research programme in Computational Biology, Barcelona Supercomputing Center, Barcelona 08034, Spain

2 Computational Bioinformatics, National Institute of Bioinformatics (INB), Barcelona 08034, Spain

3 Bioinformatics Knowledge Unit, The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion, Haifa 32000, Israel

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BMC Bioinformatics 2011, 12:378  doi:10.1186/1471-2105-12-378

Published: 26 September 2011

Abstract

Background

Protein-protein interactions are involved in most cellular processes, and their detailed physico-chemical and structural characterization is needed in order to understand their function at the molecular level. In-silico docking tools can complement experimental techniques, providing three-dimensional structural models of such interactions at atomic resolution. In several recent studies, protein structures have been modeled as networks (or graphs), where the nodes represent residues and the connecting edges their interactions. From such networks, it is possible to calculate different topology-based values for each of the nodes, and to identify protein regions with high centrality scores, which are known to positively correlate with key functional residues, hot spots, and protein-protein interfaces.

Results

Here we show that this correlation can be efficiently used for the scoring of rigid-body docking poses. When integrated into the pyDock energy-based docking method, the new combined scoring function significantly improved the results of the individual components as shown on a standard docking benchmark. This improvement was particularly remarkable for specific protein complexes, depending on the shape, size, type, or flexibility of the proteins involved.

Conclusions

The network-based representation of protein structures can be used to identify protein-protein binding regions and to efficiently score docking poses, complementing energy-based approaches.

Keywords:
protein interactions; small-world networks; binding site prediction; protein-protein docking; pyDock