DiMoVo: a Voronoi tessellation-based method for discriminating crystallographic and biological protein-protein interactions.

Abstract : MOTIVATION: Knowledge of the oligomeric state of a protein is often essential for understanding its function and mechanism. Within a protein crystal, each protein monomer is in contact with many others, forming many small interfaces and a few larger ones that are biologically significant if the protein is a homodimer in solution, but not if the protein is monomeric. Telling such 'crystal dimers' from real ones remains a difficult task. RESULTS: It has already been demonstrated that the interfaces of native and non-native protein-protein complexes can be distinguished using a combination of parameters computed with a method on the Voronoi tessellation. We show in this article that the same parameters highlight significant differences between the interfaces of biological and crystal dimers. Using these parameters as descriptors in machine learning methods leads to accurate classification of specific and non-specific protein-protein interfaces. AVAILABILITY: Software is available at http://fifi.ibbmc.u-psud.fr/DiMoVo.
Type de document :
Article dans une revue
Bioinformatics, Oxford University Press (OUP), 2008, 24 (5), pp.652-8. 〈http://bioinformatics.oxfordjournals.org/cgi/reprint/24/5/652.pdf〉. 〈10.1093/bioinformatics/btn022〉
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Contributeur : Julie Bernauer <>
Soumis le : jeudi 12 novembre 2009 - 19:31:15
Dernière modification le : jeudi 11 janvier 2018 - 06:19:23

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Julie Bernauer, Ranjit Prasad Bahadur, Francis Rodier, Joël Janin, Anne Poupon. DiMoVo: a Voronoi tessellation-based method for discriminating crystallographic and biological protein-protein interactions.. Bioinformatics, Oxford University Press (OUP), 2008, 24 (5), pp.652-8. 〈http://bioinformatics.oxfordjournals.org/cgi/reprint/24/5/652.pdf〉. 〈10.1093/bioinformatics/btn022〉. 〈inria-00431696〉

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