title: Genome-wide prediction of SH2 domain targets using structural information and the FoldX algorithm.
abstract: Current experiments likely cover only a fraction of all protein-protein interactions. Here, we developed a method to predict SH2-mediated protein-protein interactions using the structure of SH2-phosphopeptide complexes and the FoldX algorithm. We show that our approach performs similarly to experimentally derived consensus sequences and substitution matrices at predicting known in vitro and in vivo targets of SH2 domains. We use our method to provide a set of high-confidence interactions for human SH2 domains with known structure filtered on secondary structure and phosphorylation state. We validated the predictions using literature-derived SH2 interactions and a probabilistic score obtained from a naive Bayes integration of information on coexpression, conservation of the interaction in other species, shared interaction partners, and functions. We show how our predictions lead to a new hypothesis for the role of SH2 domains in signaling.
authors.affiliation: European Molecular Biology Laboratory, Heidelberg, Germany.
authors.forename: Ignacio E
authors.initials: IE
authors.lastname: Sánchez
authors.forename: Pedro
authors.initials: P
authors.lastname: Beltrao
authors.forename: Francois
authors.initials: F
authors.lastname: Stricher
authors.forename: Joost
authors.initials: J
authors.lastname: Schymkowitz
authors.forename: Jesper
authors.initials: J
authors.lastname: Ferkinghoff-Borg
authors.forename: Frederic
authors.initials: F
authors.lastname: Rousseau
authors.forename: Luis
authors.initials: L
authors.lastname: Serrano
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001665:Binding Sites; D002874:Chromosome Mapping / Q000379:methods*; D008969:Molecular Sequence Data; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D018909:src Homology Domains; D019061:src-Family Kinases / Q000737:chemistry*
chemical_list: D019061:src-Family Kinases