ArticleGenome research2003
Multimeric threading-based prediction of protein-protein interactions on a genomic scale: application to the Saccharomyces cerevisiae proteome.
Article in Genome research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- Computational Network Inference for Bacterial Interactomics.mSystems · 2022Review
- Template-based prediction of protein function.Current opinion in structural biology · 2015Review
- A rapid and efficient immunoenzymatic assay to detect receptor protein interactions: G protein-coupled receptors.International journal of molecular sciences · 2014Article
- Template-based structure modeling of protein-protein interactions.Current opinion in structural biology · 2014Review
- Template-constrained macrocyclic peptides prepared from native, unprotected precursors.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Mapping monomeric threading to protein-protein structure prediction.Journal of chemical information and modeling · 2013Article
- Novel insights through the integration of structural and functional genomics data with protein networks.Journal of structural biology · 2012Article
- The distribution of ligand-binding pockets around protein-protein interfaces suggests a general mechanism for pocket formation.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Bayesian inference for genomic data integration reduces misclassification rate in predicting protein-protein interactions.PLoS computational biology · 2011Article
- Struct2Net: a web service to predict protein-protein interactions using a structure-based approach.Nucleic acids research · 2010Article
- A threading-based method for the prediction of DNA-binding proteins with application to the human genome.PLoS computational biology · 2009Article
- Identification of protein-protein interactions and topologies in living cells with chemical cross-linking and mass spectrometry.Molecular & cellular proteomics : MCP · 2009Article
- Homology modelling of protein-protein complexes: a simple method and its possibilities and limitations.BMC bioinformatics · 2008Article
- M-TASSER: an algorithm for protein quaternary structure prediction.Biophysical journal · 2008Article
- Fold assessment for comparative protein structure modeling.Protein science : a publication of the Protein Society · 2007Article
- Structure-templated predictions of novel protein interactions from sequence information.PLoS computational biology · 2007Article
- 3D-partner: a web server to infer interacting partners and binding models.Nucleic acids research · 2007Article
- High-throughput identification of interacting protein-protein binding sites.BMC bioinformatics · 2007Article
- InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale.Genome biology · 2007Article
- Prediction of interacting proteins from homology-modeled complex structures using sequence and structure scores.Biophysics (Nagoya-shi, Japan) · 2007Article
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4 authors.
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Abstract
MULTIPROSPECTOR, a multimeric threading algorithm for the prediction of protein-protein interactions, is applied to the genome of Saccharomyces cerevisiae. Each possible pairwise interaction among more than 6000 encoded proteins is evaluated against a dimer database of 768 complex structures by using a confidence estimate of the fold assignment and the magnitude of the statistical interfacial potentials. In total, 7321 interactions between pairs of different proteins are predicted, based on 304 complex structures. Quality estimation based on the coincidence of subcellular localizations and biological functions of the predicted interactors shows that our approach ranks third when compared with all other large-scale methods. Unlike other in silico methods, MULTIPROSPECTOR is able to identify the residues that participate directly in the interaction. Three hundred seventy-four of our predictions can be found by at least one of the other studies, which is compatible with the overlap between two different other methods. From the analysis of the mRNA abundance data, our method does not bias towards proteins with high abundance. Finally, several relevant predictions involved in various functions are presented. In summary, we provide a novel approach to predict protein-protein interactions on a genomic scale that is a useful complement to experimental methods.
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