ArticlePLoS computational biology2008
Genome-wide prediction of SH2 domain targets using structural information and the FoldX algorithm.
Article in PLoS computational biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Heterologous synthesis of a simplified nitrogenase analog inScience advances · 2025Article
- Discovery and Characterization of Linear Motif Mediated Protein-Protein Complexes.Advances in experimental medicine and biology · 2024Article
- Computational Methods and Deep Learning for Elucidating Protein Interaction Networks.Methods in molecular biology (Clifton, N.J.) · 2023Article
- New analysis pipeline for high-throughput domain-peptide affinity experiments improves SH2 interaction data.The Journal of biological chemistry · 2020Article
- Adaption of human antibody λ and κ light chain architectures to CDR repertoires.Protein engineering, design & selection : PEDS · 2019Article
- Characterization of recombinant endo-1,4-β-xylanase of Bacillus halodurans C-125 and rational identification of hot spot amino acid residues responsible for enhancing thermostability by an in-silico approach.Molecular biology reports · 2019Article
- FoldX as Protein Engineering Tool: Better Than Random Based Approaches?Computational and structural biotechnology journal · 2018Review
- Enriching Peptide Libraries for Binding Affinity and Specificity Through Computationally Directed Library Design.Methods in molecular biology (Clifton, N.J.) · 2017Article
- AB-Bind: Antibody binding mutational database for computational affinity predictions.Protein science : a publication of the Protein Society · 2016Article
- Mutations in the KDM5C ARID Domain and Their Plausible Association with Syndromic Claes-Jensen-Type Disease.International journal of molecular sciences · 2015Article
- Systematic discovery of linear binding motifs targeting an ancient protein interaction surface on MAP kinases.Molecular systems biology · 2015Article
- Predicting peptide-mediated interactions on a genome-wide scale.PLoS computational biology · 2015Article
- Phosphorylation by PINK1 releases the UBL domain and initializes the conformational opening of the E3 ubiquitin ligase Parkin.PLoS computational biology · 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
- Predicting PDZ domain mediated protein interactions from structure.BMC bioinformatics · 2013Article
- Positively selected sites in cetacean myoglobins contribute to protein stability.PLoS computational biology · 2013Article
- Semi-supervised prediction of SH2-peptide interactions from imbalanced high-throughput data.PloS one · 2013Article
- Predictive Bcl-2 family binding models rooted in experiment or structure.Journal of molecular biology · 2012Article
- PDZ domain-containing 1 (PDZK1) protein regulates phospholipase C-β3 (PLC-β3)-specific activation of somatostatin by forming a ternary complex with PLC-β3 and somatostatin receptors.The Journal of biological chemistry · 2012Article
- A regression framework incorporating quantitative and negative interaction data improves quantitative prediction of PDZ domain-peptide interaction from primary sequence.Bioinformatics (Oxford, England) · 2011Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Current experiments likely cover only a fraction of all protein-protein interactions. Here, we developed a method to predict SH2-mediated protein-protein interactions using the structure of SH2-phosphopeptide complexes and the FoldX algorithm. We show that our approach performs similarly to experimentally derived consensus sequences and substitution matrices at predicting known in vitro and in vivo targets of SH2 domains. We use our method to provide a set of high-confidence interactions for human SH2 domains with known structure filtered on secondary structure and phosphorylation state. We validated the predictions using literature-derived SH2 interactions and a probabilistic score obtained from a naive Bayes integration of information on coexpression, conservation of the interaction in other species, shared interaction partners, and functions. We show how our predictions lead to a new hypothesis for the role of SH2 domains in signaling.
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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.