2016
DOI: 10.1073/pnas.1607570113
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Simultaneous identification of specifically interacting paralogs and interprotein contacts by direct coupling analysis

Abstract: Understanding protein−protein interactions is central to our understanding of almost all complex biological processes. Computational tools exploiting rapidly growing genomic databases to characterize protein−protein interactions are urgently needed. Such methods should connect multiple scales from evolutionary conserved interactions between families of homologous proteins, over the identification of specifically interacting proteins in the case of multiple paralogs inside a species, down to the prediction of r… Show more

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Cited by 127 publications
(185 citation statements)
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“…Eukaryotic complexes present a paradoxical scenario: Large families of eukaryotic proteins are the result of duplicationbased expansions, but these duplications make uncertain which paralogues of one family interact with which ones of the other. In the future, improvements aimed to disentangle the network of paralogous interactions will be fundamental to deal with eukaryotic interactions (44)(45)(46)(47). Our approach, based on preferential conservation, tackles this problem for proteins with prokaryotic homologs by looking at very divergent, well-populated, and easy-to-couple pairs of interacting prokaryotic proteins.…”
Section: Discussionmentioning
confidence: 99%
“…Eukaryotic complexes present a paradoxical scenario: Large families of eukaryotic proteins are the result of duplicationbased expansions, but these duplications make uncertain which paralogues of one family interact with which ones of the other. In the future, improvements aimed to disentangle the network of paralogous interactions will be fundamental to deal with eukaryotic interactions (44)(45)(46)(47). Our approach, based on preferential conservation, tackles this problem for proteins with prokaryotic homologs by looking at very divergent, well-populated, and easy-to-couple pairs of interacting prokaryotic proteins.…”
Section: Discussionmentioning
confidence: 99%
“…To extend protein-protein interaction prediction to a proteomic level, new algorithms have been devised to systematically identify protein-protein interactions [95,96]. Both studies used TCS as a benchmark case because of their rich sequence information and known interaction pairing.…”
Section: Protein-protein Interactionsmentioning
confidence: 99%
“…The best scoring test protein pairs are considered correct and then added to the training set and the process is repeated. This iterative approach is rather robust as it can be done with no training set [95] or without ever recalculating the interaction energy of the training set to throw out outlier matched pairs [96]. These algorithms were extended to subunits of ABC transporters [95] and to members of the tryptophan biosynthesis machinery [96] and they will likely be generally applicable to determine whether two proteins interact, as long as enough sequence information is available.…”
Section: Protein-protein Interactionsmentioning
confidence: 99%
“…The two methods, mentioned in the Introduction [4, 5], that directly maximise the strength of the predicted contacts are evaluated below. Given limitations on computer time, this comparison is not an exhaustive benchmark but is sufficient to give a clear indication of the relative performance of the methods.…”
Section: Resultsmentioning
confidence: 99%
“…The problem of paralog matching has recently been approached more directly by two similar methods that maximise the strength of the predicted contacts while iteratively introducing paralog pairings [4, 5]. Although only tested on a few examples, these methods give encouraging results but are limited by the heavy cost of continually recomputing the contacts.…”
Section: Introductionmentioning
confidence: 99%