ArticleNucleic acids research2008
Global investigation of protein-protein interactions in yeast Saccharomyces cerevisiae using re-occurring short polypeptide sequences.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Sequence-Based Protein-Protein Interaction Prediction and Its Applications in Drug Discovery.Cells · 2025Review
- Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments.Chemical reviews · 2024Review
- A computational approach to rapidly design peptides that detect SARS-CoV-2 surface protein S.NAR genomics and bioinformatics · 2022Article
- Reciprocal Perspective for Improved Protein-Protein Interaction Prediction.Scientific reports · 2018Article
- SPRINT: ultrafast protein-protein interaction prediction of the entire human interactome.BMC bioinformatics · 2017Article
- TRI_tool: a web-tool for prediction of protein-protein interactions in human transcriptional regulation.Bioinformatics (Oxford, England) · 2017Article
- Evolution of protein-protein interaction networks in yeast.PloS one · 2017Article
- Predicting protein-protein interactions via multivariate mutual information of protein sequences.BMC bioinformatics · 2016Article
- Efficient prediction of human protein-protein interactions at a global scale.BMC bioinformatics · 2014Article
- Homology-based prediction of interactions between proteins using Averaged One-Dependence Estimators.BMC bioinformatics · 2014Article
- Article
- Short Co-occurring Polypeptide Regions Can Predict Global Protein Interaction Maps.Scientific reports · 2012Article
- Revisiting the negative example sampling problem for predicting protein-protein interactions.Bioinformatics (Oxford, England) · 2011Article
- Binding site prediction for protein-protein interactions and novel motif discovery using re-occurring polypeptide sequences.BMC bioinformatics · 2011Article
- Chemical-genetic profile analysis of five inhibitory compounds in yeast.BMC chemical biology · 2010Article
- Pandora, a pathway and network discovery approach based on common biological evidence.Bioinformatics (Oxford, England) · 2010Article
- Critical assessment of sequence-based protein-protein interaction prediction methods that do not require homologous protein sequences.BMC bioinformatics · 2009Article
- A genetic screen in Saccharomyces cerevisiae identifies new genes that interact with mex67-5, a temperature-sensitive allele of the gene encoding the mRNA export receptor.Molecular genetics and genomics : MGG · 2009Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Protein-protein interaction (PPI) maps provide insight into cellular biology and have received considerable attention in the post-genomic era. While large-scale experimental approaches have generated large collections of experimentally determined PPIs, technical limitations preclude certain PPIs from detection. Recently, we demonstrated that yeast PPIs can be computationally predicted using re-occurring short polypeptide sequences between known interacting protein pairs. However, the computational requirements and low specificity made this method unsuitable for large-scale investigations. Here, we report an improved approach, which exhibits a specificity of approximately 99.95% and executes 16,000 times faster. Importantly, we report the first all-to-all sequence-based computational screen of PPIs in yeast, Saccharomyces cerevisiae in which we identify 29,589 high confidence interactions of approximately 2 x 10(7) possible pairs. Of these, 14,438 PPIs have not been previously reported and may represent novel interactions. In particular, these results reveal a richer set of membrane protein interactions, not readily amenable to experimental investigations. From the novel PPIs, a novel putative protein complex comprised largely of membrane proteins was revealed. In addition, two novel gene functions were predicted and experimentally confirmed to affect the efficiency of non-homologous end-joining, providing further support for the usefulness of the identified PPIs in biological investigations.
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