ArticleJournal of molecular biology2023
PrePPI: A Structure Informed Proteome-wide Database of Protein-Protein Interactions.
Article in Journal of molecular biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- PrePPI - Structure-based Prediction of Protein-protein Interactomes and Networks.Journal of molecular biology · 2026Article
- ProteomeLM: A proteome-scale language model enables accurate and rapid prediction of protein-protein interactions and gene essentiality across taxa.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- AlphaFold-driven discovery of oxysterol-binding protein-related protein-phosphoinositide 3-, 4-, and 5-phosphatase interactions using new generation confidence scores.Protein science : a publication of the Protein Society · 2026Article
- Proteome-wide prediction of interactions between structured domains and peptide motifs reveals functionally coherent subnetworks.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Combining structural modeling and deep learning to calculate the E. coli protein interactome and functional networks.Nature communications · 2026Article
- A Multiscale Computational Architecture to Study Signaling Dynamics at Cell-Cell Interfaces.bioRxiv : the preprint server for biology · 2026Article
- Predicting Protein-Protein Interactions from Machine-Learned Representations.Advances in experimental medicine and biology · 2026Review
- Predicting protein-protein interactions in the human proteome.Science (New York, N.Y.) · 2025Article
- Memory-efficient, accelerated protein interaction inference with blocked, multi-GPU D-SCRIPT.Bioinformatics (Oxford, England) · 2025Article
- Bacterial Systematic Genetics and Integrated Multi-Omics: Beyond Static Genomics Toward Predictive Models.International journal of molecular sciences · 2025Review
- A structurally informed human protein-protein interactome reveals proteome-wide perturbations caused by disease mutations.Nature biotechnology · 2025Article
- Structure-Based Approaches for Protein-Protein Interaction Prediction Using Machine Learning and Deep Learning.Biomolecules · 2025Review
- FunCoup 6: advancing functional association networks across species with directed links and improved user experience.Nucleic acids research · 2025Article
- Deep learning identification of novel autophagic protein-protein interactions and experimental validation of Beclin 2-Ubiquilin 1 axis in triple-negative breast cancer.Oncology research · 2025Article
- Exploring the role of EBV in multiple sclerosis pathogenesis through EBV interactome.Frontiers in immunology · 2025Article
- Multimeric protein interaction and complex prediction: Structure, dynamics and function.Computational and structural biotechnology journal · 2025Review
- Improved protein interaction models predict differences in complexes between human cell lines.bioRxiv : the preprint server for biology · 2024Article
- MAGPIE: An interactive tool for visualizing and analyzing protein-ligand interactions.Protein science : a publication of the Protein Society · 2024Article
- SLiMAn 2.0: meaningful navigation through peptide-protein interaction networks.Nucleic acids research · 2024Article
- ZEPPI: Proteome-scale sequence-based evaluation of protein-protein interaction models.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
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Authors and funding
5 authors.
Funding
Abstract
We present an updated version of the Predicting Protein-Protein Interactions (PrePPI) webserver which predicts PPIs on a proteome-wide scale. PrePPI combines structural and non-structural evidence within a Bayesian framework to compute a likelihood ratio (LR) for essentially every possible pair of proteins in a proteome; the current database is for the human interactome. The structural modeling (SM) component is derived from template-based modeling and its application on a proteome-wide scale is enabled by a unique scoring function used to evaluate a putative complex. The updated version of PrePPI leverages AlphaFold structures that are parsed into individual domains. As has been demonstrated in earlier applications, PrePPI performs extremely well as measured by receiver operating characteristic curves derived from testing on E. coli and human protein-protein interaction (PPI) databases. A PrePPI database of ∼1.3 million human PPIs can be queried with a webserver application that comprises multiple functionalities for examining query proteins, template complexes, 3D models for predicted complexes, and related features (https://honiglab.c2b2.columbia.edu/PrePPI). PrePPI is a state-of-the-art resource that offers an unprecedented structure-informed view of the human interactome.
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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.