ArticleNucleic acids research2013
PrePPI: a structure-informed database of protein-protein interactions.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 113 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
113 citing papers in PubMed.
- PrePPI - Structure-based Prediction of Protein-protein Interactomes and Networks.Journal of molecular biology · 2026Article
- HBx-mediated GPT2 suppression promotes liver cancer development by downregulating ADH1A.Cancer biology & medicine · 2026Article
- Ohno-miRNAs: miRNA pairs derived from whole-genome duplication.PLoS computational biology · 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
- Machine Learning for Protein Function Prediction.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Bioinformatic Resources for Exploring Human-virus Protein-protein Interactions Based on Binding Modes.Genomics, proteomics & bioinformatics · 2024Review
- Inhibition of GLUD1 mediated by LASP1 and SYVN1 contributes to hepatitis B virus X protein-induced hepatocarcinogenesis.Journal of molecular cell biology · 2024Article
- RNA 5-methylcytosine marks mitochondrial double-stranded RNAs for degradation and cytosolic release.Molecular cell · 2024Article
- Hepatitis B virus core protein stabilizes RANGAP1 to upregulate KDM2A and facilitate hepatocarcinogenesis.Cellular oncology (Dordrecht, Netherlands) · 2024Article
- Bifunctional Inhibitor Reveals NEK2 as a Therapeutic Target and Regulator of Oncogenic Pathways in Lymphoma.Molecular cancer therapeutics · 2024Article
- Fast and scalable querying of eukaryotic linear motifs with gget elm.Bioinformatics (Oxford, England) · 2024Article
- Structural coverage of the human interactome.Briefings in bioinformatics · 2023Article
- From observational to actionable: rethinking omics in biologics production.Trends in biotechnology · 2023Review
- Elucidation of genome-wide understudied proteins targeted by PROTAC-induced degradation using interpretable machine learning.PLoS computational biology · 2023Article
- Identification of glycogen phosphorylase L as a potential target for lung cancer.Medical oncology (Northwood, London, England) · 2023Article
- Narrow funnel-like interaction energy distribution is an indicator of specific protein interaction partner.iScience · 2023Article
- SVSBI: sequence-based virtual screening of biomolecular interactions.Communications biology · 2023Article
- Hepatitis B virus X protein promotes MAN1B1 expression by enhancing stability of GRP78 via TRIM25 to facilitate hepatocarcinogenesis.British journal of cancer · 2023Article
- The structural flexibility of MAD1 facilitates the assembly of the Mitotic Checkpoint Complex.Nature communications · 2023Article
- Gene transferability and sociality do not correlate with gene connectivity.Proceedings. Biological sciences · 2022Article
53 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
PrePPI (http://bhapp.c2b2.columbia.edu/PrePPI) is a database that combines predicted and experimentally determined protein-protein interactions (PPIs) using a Bayesian framework. Predicted interactions are assigned probabilities of being correct, which are derived from calculated likelihood ratios (LRs) by combining structural, functional, evolutionary and expression information, with the most important contribution coming from structure. Experimentally determined interactions are compiled from a set of public databases that manually collect PPIs from the literature and are also assigned LRs. A final probability is then assigned to every interaction by combining the LRs for both predicted and experimentally determined interactions. The current version of PrePPI contains ∼2 million PPIs that have a probability more than ∼0.1 of which ∼60 000 PPIs for yeast and ∼370 000 PPIs for human are considered high confidence (probability > 0.5). The PrePPI database constitutes an integrated resource that enables users to examine aggregate information on PPIs, including both known and potentially novel interactions, and that provides structural models for many of the PPIs.
Indexed as
Identifiers
What OpenQuestion 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 OpenQuestion graph.