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Issue 11, 2010
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Yeast proteinprotein interaction binding sites: prediction from the motif–motif, motif–domain and domain–domain levels

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Abstract

Interacting proteins can contact with each other at three different levels: by a domain binding to another domain, by a domain binding to a short protein motif, or by a motif binding to another motif. In our previous work, we proposed an approach to predict motif–motif binding sites for the yeast interactome by contrasting high-quality positive interactions and high-quality non-interactions using a simple statistical analysis. Here, we extend this idea to more comprehensively infer binding sites, including domain–domain, domain–motif, and motif–motif interactions. In this study, we integrated 2854 yeast proteins that undergo 13 531 high-quality interactions and 3491 yeast proteins undergoing 578 459 high-quality non-interactions. Overall, we found 6315 significant binding site pairs involving 2371 domains and 637 motifs. Benchmarked using the iPfam, DIP CORE, and MIPS, our inferred results are reliable. Interestingly, some of our predicted binding site pairs may, at least in the yeast genome, guide researchers to assay novel proteinprotein interactions by mutagenesis or other experiments. Our work demonstrates that by inferring significant proteinprotein binding sites at an aggregate level combining domain–domain, domain–motif and motif–motif levels based on high-quality positive and negative datasets, this method may be capable of identifying the binding site pairs that mediate proteinprotein interactions.

Graphical abstract: Yeast protein–protein interaction binding sites: prediction from the motif–motif, motif–domain and domain–domain levels

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Publication details

The article was received on 07 Jun 2010, accepted on 16 Jul 2010 and first published on 17 Aug 2010


Article type: Paper
DOI: 10.1039/C0MB00038H
Citation: Mol. BioSyst., 2010,6, 2164-2173
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    Yeast proteinprotein interaction binding sites: prediction from the motif–motif, motif–domain and domain–domain levels

    E. Pang and K. Lin, Mol. BioSyst., 2010, 6, 2164
    DOI: 10.1039/C0MB00038H

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