title: Predicting protein-protein interaction by the mirrortree method: possibilities and limitations.
abstract: Molecular co-evolution analysis as a sequence-only based method has been used to predict protein-protein interactions. In co-evolution analysis, Pearson's correlation within the mirrortree method is a well-known way of quantifying the correlation between protein pairs. Here we studied the mirrortree method on both known interacting protein pairs and sets of presumed non-interacting protein pairs, to evaluate the utility of this correlation analysis method for predicting protein-protein interactions within eukaryotes. We varied metrics for computing evolutionary distance and evolutionary span of the species analyzed. We found the differences between co-evolutionary correlation scores of the interacting and non-interacting proteins, normalized for evolutionary span, to be significantly predictive for proteins conserved over a wide range of eukaryotic clades (from mammals to fungi). On the other hand, for narrower ranges of evolutionary span, the predictive power was much weaker.
authors.affiliation: Department of Biochemistry, University of Illinois, Urbana-Champaign, Illinois, United States of America.
authors.forename: Hua
authors.initials: H
authors.lastname: Zhou
authors.affiliation: Department of Biochemistry, University of Illinois, Urbana-Champaign, Illinois, United States of America ; Beckman Institute, National Center for Supercomputing Applications, Program in Biophysics and Computational Biology, Department of Molecular and Integrative Physiology, University of Illinois, Urbana-Champaign, Illinois, United States of America.
authors.forename: Eric
authors.initials: E
authors.lastname: Jakobsson
mesh_terms: D019143:Evolution, Molecular; D011485:Protein Binding; D025941:Protein Interaction Mapping