ArticleNucleic acids research2008
Prediction of phosphotyrosine signaling networks using a scoring matrix-assisted ligand identification approach.
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 27 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
27 citing papers in PubMed, 52 citations in OpenAlex.
- Accurate affinity models for SH2 domains from peptide binding assays and free-energy regression.Protein science : a publication of the Protein Society · 2025Article
- Article
- iPhosY-PseAAC: identify phosphotyrosine sites by incorporating sequence statistical moments into PseAAC.Molecular biology reports · 2018Article
- Interactome Mapping Uncovers a General Role for Numb in Protein Kinase Regulation.Molecular & cellular proteomics : MCP · 2018Article
- Identification and characterization of a large family of superbinding bacterial SH2 domains.Nature communications · 2018Article
- PSSMSearch: a server for modeling, visualization, proteome-wide discovery and annotation of protein motif specificity determinants.Nucleic acids research · 2018Article
- Using oriented peptide array libraries to evaluate methylarginine-specific antibodies and arginine methyltransferase substrate motifs.Scientific reports · 2016Article
- Tyrosine phosphorylation of RAS by ABL allosterically enhances effector binding.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2015Article
- Article
- T cell specific adaptor protein (TSAd) promotes interaction of Nck with Lck and SLP-76 in T cells.Cell communication and signaling : CCS · 2015Article
- Non-histone protein methylation as a regulator of cellular signalling and function.Nature reviews. Molecular cell biology · 2015Review
- A multiscale statistical mechanical framework integrates biophysical and genomic data to assemble cancer networks.Nature genetics · 2014Article
- The development and application of a quantitative peptide microarray based approach to protein interaction domain specificity space.Molecular & cellular proteomics : MCP · 2014Article
- Enhanced prediction of Src homology 2 (SH2) domain binding potentials using a fluorescence polarization-derived c-Met, c-Kit, ErbB, and androgen receptor interactome.Molecular & cellular proteomics : MCP · 2014Article
- A method for systematic mapping of protein lysine methylation identifies functions for HP1β in DNA damage response.Molecular cell · 2013Article
- Tyrosine 132 phosphorylation of influenza A virus M1 protein is crucial for virus replication by controlling the nuclear import of M1.Journal of virology · 2013Article
- Semi-supervised prediction of SH2-peptide interactions from imbalanced high-throughput data.PloS one · 2013Article
- The application of modular protein domains in proteomics.FEBS letters · 2012Review
- The human phosphotyrosine signaling network: evolution and hotspots of hijacking in cancer.Genome research · 2012Article
- The identification of short linear motif-mediated interfaces within the human interactome.Bioinformatics (Oxford, England) · 2012Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Systematic identification of binding partners for modular domains such as Src homology 2 (SH2) is important for understanding the biological function of the corresponding SH2 proteins. We have developed a worldwide web-accessible computer program dubbed SMALI for scoring matrix-assisted ligand identification for SH2 domains and other signaling modules. The current version of SMALI harbors 76 unique scoring matrices for SH2 domains derived from screening oriented peptide array libraries. These scoring matrices are used to search a protein database for short peptides preferred by an SH2 domain. An experimentally determined cut-off value is used to normalize an SMALI score, therefore allowing for direct comparison in peptide-binding potential for different SH2 domains. SMALI employs distinct scoring matrices from Scansite, a popular motif-scanning program. Moreover, SMALI contains built-in filters for phosphoproteins, Gene Ontology (GO) correlation and colocalization of subject and query proteins. Compared to Scansite, SMALI exhibited improved accuracy in identifying binding peptides for SH2 domains. Applying SMALI to a group of SH2 domains identified hundreds of interactions that overlap significantly with known networks mediated by the corresponding SH2 proteins, suggesting SMALI is a useful tool for facile identification of signaling networks mediated by modular domains that recognize short linear peptide motifs.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.