title: Prediction of biological protein-protein interactions using atom-type and amino acid properties.
abstract: Identification and analysis of types of biological protein-protein interactions and their interfaces to predict obligate and non-obligate complexes is a problem that has drawn the attention of the research community in the past few years. In this paper, we propose a prediction approach to predict these two types of complexes. We use desolvation energies - amino acid and atom type - of the residues present in the interface. The prediction is performed via two state-of-the-art classification techniques, namely linear dimensionality reduction (LDR) and support vector machines (SVM). The results on a newly compiled data set, namely BPPI, which is a joint and modified version of two well-known data sets consisting of 213 obligate and 303 non-obligate complexes, show that the best prediction is achieved with SVM (76.94% accuracy) when using desolvation energies of atom-type features. Also, the proposed approach outperforms the previous solvent accessible area-based approaches using SVM (75% accuracy) and LDR (73.06% accuracy). Moreover, a visual analysis of desolvation energies in obligate and non-obligate complexes shows that a few atom-type pairs are good descriptors for these types of complexes.
authors.affiliation: School of Computer Science, University of Windsor, 401 Sunset Avenue, Windsor, Ontario, Canada.
authors.forename: Md Mominul
authors.initials: MM
authors.lastname: Aziz
authors.forename: Mina
authors.initials: M
authors.lastname: Maleki
authors.forename: Luis
authors.initials: L
authors.lastname: Rueda
authors.forename: Mohammad
authors.initials: M
authors.lastname: Raza
authors.forename: Sridip
authors.initials: S
authors.lastname: Banerjee
mesh_terms: D030562:Databases, Protein; D008954:Models, Biological; D008958:Models, Molecular; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*; D060388:Support Vector Machine
chemical_list: D011506:Proteins