ArticlePloS one2013
Predicting protein-protein interaction by the mirrortree method: possibilities and limitations.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- In Silico Network Pharmacology, Molecular Docking, and Molecular Dynamics Analysis of Rosemary-Derived Compounds as Potential HSP90 Inhibitors for Cancer Therapy.Current issues in molecular biology · 2025Article
- Protein-protein interaction prediction using bidirectional GRUs with explicit ensemble.PloS one · 2025Article
- Computational Docking Reveals Co-Evolution of C4 Carbon Delivery Enzymes in Diverse Plants.International journal of molecular sciences · 2022Article
- S100A7/Ran-binding protein 9 coevolution in mammals.Immunogenetics · 2020Article
- MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions.BMC bioinformatics · 2018Article
- Proteomic and phylogenetic coevolution analyses of pM79 and pM92 identify interactions with RNA polymerase II and delineate the murine cytomegalovirus late transcription complex.The Journal of general virology · 2017Article
- Practical aspects of protein co-evolution.Frontiers in cell and developmental biology · 2014Review
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2 authors.
Funding
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.
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