NDLI: Yeast protein-protein interaction binding sites: prediction from the motif-motif, motif-domain and domain-domain levels.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Pang, Erli Lin, Kui
Description	Country affiliation: China Author Affiliation: Pang E ( State Key Laboratory of Earth Surface Processes and Resource Ecology and College of Life Sciences, Beijing Normal University, Beijing 100875, China.)
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 protein-protein interactions by mutagenesis or other experiments. Our work demonstrates that by inferring significant protein-protein 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 protein-protein interactions.
File Format	HTM / HTML
ISSN	1742206X
Issue Number	11
Volume Number	6
e-ISSN	17422051
Journal	Molecular BioSystems
Language	English
Publisher	Royal Society of Chemistry
Publisher Date	2010-11-01
Publisher Place	Great Britain (UK)
Access Restriction	Subscribed
Subject Keyword	Discipline Molecular Biology Discipline Biochemistry Protein Interaction Domains And Motifs Protein Interaction Mapping Methods Saccharomyces Cerevisiae Metabolism Binding Sites Databases, Protein Mutation Genetics Predictive Value Of Tests Protein Binding Reproducibility Of Results Journal Article Research Support, Non-u.s. Gov't
Content Type	Text
Resource Type	Article
Subject	Molecular Biology Biotechnology

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