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.
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.
Authors: Jaclyn LoPiccolo; Seung Joong Kim; Yi Shi; Bin Wu; Haiyan Wu; Brian T Chait; Robert H Singer; Andrej Sali; Michael Brenowitz; Anne R Bresnick; Jonathan M Backer Journal: J Biol Chem Date: 2015-10-16 Impact factor: 5.157
Authors: Seung Joong Kim; Javier Fernandez-Martinez; Parthasarathy Sampathkumar; Anne Martel; Tsutomu Matsui; Hiro Tsuruta; Thomas M Weiss; Yi Shi; Ane Markina-Inarrairaegui; Jeffery B Bonanno; J Michael Sauder; Stephen K Burley; Brian T Chait; Steven C Almo; Michael P Rout; Andrej Sali Journal: Mol Cell Proteomics Date: 2014-08-19 Impact factor: 5.911