ArticleNature methods2015
Quantifying domain-ligand affinities and specificities by high-throughput holdup assay.
Article in Nature methods, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
What it found
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Who cites it
51 citing papers in PubMed.
- Quantitative analysis of DNA-GATA1 binding alterations linked to hematopoietic disorders.The FEBS journal · 2026Article
- Coronavirus protein interaction mapping in bat and human cells reveals network rewiring governing immune evasion and zoonotic potential.Cell host & microbe · 2026Article
- Molecular Dynamics and Docking Reveal Enhanced Binding of HPV16 E6 Asian American Variants To non-phosphorylated DLG1.Cell biochemistry and biophysics · 2026Article
- Sequence Engineering at Non-motif Modulator Residues Yields a Peptide That Effectively Targets a Single PDZ Protein in a Disease-relevant Cellular Context.Journal of molecular biology · 2026Article
- The non-catalytic DNA polymerase ε subunit is an NPF motif recognition protein.Nature communications · 2025Article
- Article
- Sequence engineering at non-motif modulator residues yields a peptide that effectively targets a single PDZ protein in a disease-relevant cellular context.bioRxiv : the preprint server for biology · 2025Article
- A High-Throughput Investigation of the Binding Specificity of Carbohydrate-Binding Modules for Synthetic and Natural Polymers.ChemSusChem · 2025Article
- Multimodal SARS-CoV-2 interactome sketches the virus-host spatial organization.Communications biology · 2025Article
- Article
- ELM-the Eukaryotic Linear Motif resource-2024 update.Nucleic acids research · 2024Article
- The Human PDZome 2.0: Characterization of a New Resource to Test for PDZ Interactions by Yeast Two-Hybrid.Membranes · 2023Article
- Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs.Nature communications · 2023Article
- Multiplex measurement of protein-peptide dissociation constants using dialysis and mass spectrometry.Protein science : a publication of the Protein Society · 2023Article
- Additive energetic contributions of multiple peptide positions determine the relative promiscuity of viral and human sequences for PDZ domain targets.Protein science : a publication of the Protein Society · 2023Article
- Additive energetic contributions of multiple peptide positions determine the relative promiscuity of viral and human sequences for PDZ domain targets.bioRxiv : the preprint server for biology · 2023Article
- Interactions of the protein tyrosine phosphatase PTPN3 with viral and cellular partners through its PDZ domain: insights into structural determinants and phosphatase activity.Frontiers in molecular biosciences · 2023Article
- The flavagline FL3 interferes with the association of Annexin A2 with the eIF4F initiation complex and transiently stimulates the translation ofFrontiers in cell and developmental biology · 2023Article
- Native holdup (nHU) to measure binding affinities from cell extracts.Science advances · 2022Article
- The cargo adapter protein CLINT1 is phosphorylated by the Numb-associated kinase BIKE and mediates dengue virus infection.The Journal of biological chemistry · 2022Article
Corrections and comments
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Authors and funding
20 authors.
Funding
Abstract
Many protein interactions are mediated by small linear motifs interacting specifically with defined families of globular domains. Quantifying the specificity of a motif requires measuring and comparing its binding affinities to all its putative target domains. To this end, we developed the high-throughput holdup assay, a chromatographic approach that can measure up to 1,000 domain-motif equilibrium binding affinities per day. After benchmarking the approach on 210 PDZ-peptide pairs with known affinities, we determined the affinities of two viral PDZ-binding motifs derived from human papillomavirus E6 oncoproteins for 209 PDZ domains covering 79% of the human 'PDZome'. We obtained sharply sequence-dependent binding profiles that quantitatively describe the PDZome recognition specificity of each motif. This approach, applicable to many categories of domain-ligand interactions, has wide potential for quantifying the specificities of interactomes.
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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.