ArticleJournal of molecular biology2022
PEPPI: Whole-proteome Protein-protein Interaction Prediction through Structure and Sequence Similarity, Functional Association, and Machine Learning.
Article in Journal of molecular biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
31 citing papers in PubMed, 63 citations in OpenAlex.
- Proteome-informed interrogation of a methanogenic archaeon links stress response mechanisms with microbial performance and robustness during biomethanation.Engineering microbiology · 2026Article
- Immunoinformatics-guided design of a conserved multi-epitope vaccine candidate against pathogenic human coronaviruses.Naunyn-Schmiedeberg's archives of pharmacology · 2026Article
- 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
- Investigating the Role of OsHDT701 and Other Blast-Associated Negative Regulatory Genes in Indica Rice Cultivar Ranjit Using Combined Wet Lab and Computational Approaches.Molecular biotechnology · 2025Article
- TERT translocation to mitochondria: Exploring its role in mitochondrial homeostasis.PLoS genetics · 2025Article
- Sequence-Based Protein-Protein Interaction Prediction and Its Applications in Drug Discovery.Cells · 2025Review
- Light Quantity Impacts Early Response to Cold and Cold Acclimation in Young Leaves of Arabidopsis.Plant, cell & environment · 2025Article
- Recent progress and future challenges in structure-based protein-protein interaction prediction.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Review
- Structural and mechanistic diversity in p53-mediated regulation of organismal longevity across taxonomical orders.PLoS computational biology · 2025Article
- HMGB1 Regulates Adipocyte Lipolysis via Caveolin-1 Signaling: Implications for Metabolic and Cardiovascular Diseases.International journal of molecular sciences · 2025Article
- Conserved leucine-rich repeat proteins in the adhesive projectile slime of velvet worms.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Depletion of tumor-derived CXCL5 improves T cell infiltration and anti-PD-1 therapy response in an obese model of pancreatic cancer.Journal for immunotherapy of cancer · 2025Article
- Biochemical and physiological characterization of Aedes aegypti midgut chymotrypsin.Scientific reports · 2025Article
- Neuroglobin regulates autophagy through mTORC1/RAPTOR/ULK-1 pathway in human neuroblastoma cells.Scientific reports · 2025Article
- PPILS: Protein-protein interaction prediction with language of biological coding.Computers in biology and medicine · 2025Article
- Expanding the genotypic and phenotypic spectrum of EAST/SeSAME syndrome: identification of a novel homozygous mutation (c.194 G > A) in KCNJ10 gene.Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology · 2025Article
- Fine-Tuned Expression of Evolutionarily Conserved Signaling Molecules in theInternational journal of molecular sciences · 2024Article
- SpatialPPI: Three-dimensional space protein-protein interaction prediction with AlphaFold Multimer.Computational and structural biotechnology journal · 2024Article
- Benchmark Investigation of SARS-CoV-2 Mutants' Immune Escape with 2B04 Murine Antibody: A Step Towards Unraveling a Larger Picture.Current issues in molecular biology · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Proteome-wide identification of protein-protein interactions is a formidable task which has yet to be sufficiently addressed by experimental methodologies. Many computational methods have been developed to predict proteome-wide interaction networks, but few leverage both the sensitivity of structural information and the wide availability of sequence data. We present PEPPI, a pipeline which integrates structural similarity, sequence similarity, functional association data, and machine learning-based classification through a naïve Bayesian classifier model to accurately predict protein-protein interactions at a proteomic scale. Through benchmarking against a set of 798 ground truth interactions and an equal number of non-interactions, we have found that PEPPI attains 4.5% higher AUROC than the best of other state-of-the-art methods. As a proteomic-scale application, PEPPI was applied to model the interactions which occur between SARS-CoV-2 and human host cells during coronavirus infection, where 403 high-confidence interactions were identified with predictions covering 73% of a gold standard dataset from PSICQUIC and demonstrating significant complementarity with the most recent high-throughput experiments. PEPPI is available both as a webserver and in a standalone version and should be a powerful and generally applicable tool for computational screening of protein-protein interactions.
Indexed as
Identifiers
What Socratic holds
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.