ArticleMolecular systems biology2020
Large-scale survey and database of high affinity ligands for peptide recognition modules.
Article in Molecular systems biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Ki-67 regulates heterochromatin organization in neurons and forms condensates with heterochromatic components.Nature communications · 2026Article
- Seven complete comparative maps of allosteric mutations in a protein family.Nature communications · 2026Article
- Several plant self-incompatibility systems may be controlled by atypical receptor-ligand interactions.The Plant journal : for cell and molecular biology · 2026Review
- A protein-fragment complementation assay to quantify synthetic protein scaffold efficiency.Synthetic biology (Oxford, England) · 2026Article
- Article
- Accurate affinity models for SH2 domains from peptide binding assays and free-energy regression.Protein science : a publication of the Protein Society · 2025Article
- Deep learning molecular interaction motifs from receptor structures alone.Journal of cheminformatics · 2025Article
- Article
- Immunopeptides: immunomodulatory strategies and prospects for ocular immunity applications.Frontiers in immunology · 2024Review
- Cell-Penetrating Milk-Derived Peptides with a Non-Inflammatory Profile.Molecules (Basel, Switzerland) · 2023Article
- Large-scale phosphomimetic screening identifies phospho-modulated motif-based protein interactions.Molecular systems biology · 2023Article
- Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs.Nature communications · 2023Article
- Peptide-binding specificity prediction using fine-tuned protein structure prediction networks.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Orchestrating serine/threonine phosphorylation and elucidating downstream effects by short linear motifs.The Biochemical journal · 2022Review
- Proteome-scale mapping of binding sites in the unstructured regions of the human proteome.Molecular systems biology · 2022Article
- Discovery of an exosite on the SOCS2-SH2 domain that enhances SH2 binding to phosphorylated ligands.Nature communications · 2021Article
- Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 specific mechanisms and vulnerabilities.Nature communications · 2021Article
- Systems Biology to Understand and Regulate Human Retroviral Proinflammatory Response.Frontiers in immunology · 2021Review
- Large-scale survey and database of high affinity ligands for peptide recognition modules.Molecular systems biology · 2020Article
Corrections and comments
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Authors and funding
14 authors.
Funding
Abstract
Many proteins involved in signal transduction contain peptide recognition modules (PRMs) that recognize short linear motifs (SLiMs) within their interaction partners. Here, we used large-scale peptide-phage display methods to derive optimal ligands for 163 unique PRMs representing 79 distinct structural families. We combined the new data with previous data that we collected for the large SH3, PDZ, and WW domain families to assemble a database containing 7,984 unique peptide ligands for 500 PRMs representing 82 structural families. For 74 PRMs, we acquired enough new data to map the specificity profiles in detail and derived position weight matrices and binding specificity logos based on multiple peptide ligands. These analyses showed that optimal peptide ligands resembled peptides observed in existing structures of PRM-ligand complexes, indicating that a large majority of the phage-derived peptides are likely to target natural peptide-binding sites and could thus act as inhibitors of natural protein-protein interactions. The complete dataset has been assembled in an online database (http://www.prm-db.org) that will enable many structural, functional, and biological studies of PRMs and SLiMs.
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