Predicting protein interaction sites: binding hot-spots in protein--protein and protein--ligand interfaces

Authors:
Nicholas J. Burgoyne;Richard M. Jackson
Affiliations:
Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds Leeds LS2 9JT, UK;Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds Leeds LS2 9JT, UK
Venue:
Bioinformatics
Year:
2006

Citing 0
Cited 2

Prediction of protein-protein interaction sites by using autocorrelation descriptor and support vector machine

ICIC'10 Proceedings of the Advanced intelligent computing theories and applications, and 6th international conference on Intelligent computing
Informatics-driven Protein-protein Docking

Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics

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Abstract

Motivation: Protein assemblies are currently poorly represented in structural databases and their structural elucidation is a key goal in biology. Here we analyse clefts in protein surfaces, likely to correspond to binding 'hot-spots', and rank them according to sequence conservation and simple measures of physical properties including hydrophobicity, desolvation, electrostatic and van der Waals potentials, to predict which are involved in binding in the native complex. Results: The resulting differences between predicting binding-sites at protein--protein and protein--ligand interfaces are striking. There is a high level of prediction accuracy (≤93%) for protein--ligand interactions, based on the following attributes: van der Waals potential, electrostatic potential, desolvation and surface conservation. Generally, the prediction accuracy for protein--protein interactions is lower, with the exception of enzymes. Our results show that the ease of cleft desolvation is strongly predictive of interfaces and strongly maintained across all classes of protein-binding interface. Contact: r.m.jackson@leeds.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.