ArticleDatabase : the journal of biological databases and curation2019
APID database: redefining protein-protein interaction experimental evidences and binary interactomes.
Article in Database : the journal of biological databases and curation, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.
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83 citing papers in PubMed.
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- The aging genome exhibits organized vulnerability to somatic mutations.bioRxiv : the preprint server for biology · 2026Article
- Functional flexibility in bacterial hub proteins is driven by proteome expansion.Scientific reports · 2026Article
- Strategies for constructing context-specific protein-protein interaction networks.Briefings in bioinformatics · 2026Review
- 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
- IID 2025: Physical protein interaction data with detection types, co-purified protein sets, molecular docking, and immune cell networks.Nucleic acids research · 2026Article
- A Multi-level Perspective on the Evolution of Orthologs and Their Functions.Journal of molecular evolution · 2025Review
- When neighbors play a role: A systems-level analysis of protein interactions conditioning cancer driver mutation effects.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Topology-driven negative sampling enhances generalizability in protein-protein interaction prediction.Bioinformatics (Oxford, England) · 2025Article
- New Insights and Implications of Cell-Cell Interactions in Developmental Biology.International journal of molecular sciences · 2025Review
- A collaborative network analysis for the interpretation of transcriptomics data in Huntington's disease.Scientific reports · 2025Article
- Acrylamide and bisphenol A: two plastic additives increase platelet activation, via oxidative stress.Frontiers in pharmacology · 2025Article
- konnect2prot 2.0: Integrating advanced analytical tools for deeper understanding of protein properties in a functional protein-protein interaction network.Computational and structural biotechnology journal · 2025Article
- Target repositioning using multi-layer networks and machine learning: The case of prostate cancer.Computational and structural biotechnology journal · 2024Article
- Heterogeneous network approaches to protein pathway prediction.Computational and structural biotechnology journal · 2024Review
- Rapid profiling of transcription factor-cofactor interaction networks reveals principles of epigenetic regulation.Nucleic acids research · 2024Article
- MOCHA's advanced statistical modeling of scATAC-seq data enables functional genomic inference in large human cohorts.Nature communications · 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
- System-level analysis of genes mutated in muscular dystrophies reveals a functional pattern associated with muscle weakness distribution.Scientific reports · 2024Article
23 more citing papers are in PubMed but not listed here.
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7 authors.
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Abstract
The collection and integration of all the known protein-protein physical interactions within a proteome framework are critical to allow proper exploration of the protein interaction networks that drive biological processes in cells at molecular level. APID Interactomes is a public resource of biological data (http://apid.dep.usal.es) that provides a comprehensive and curated collection of `protein interactomes' for more than 1100 organisms, including 30 species with more than 500 interactions, derived from the integration of experimentally detected protein-to-protein physical interactions (PPIs). We have performed an update of APID database including a redefinition of several key properties of the PPIs to provide a more precise data integration and to avoid false duplicated records. This includes the unification of all the PPIs from five primary databases of molecular interactions (BioGRID, DIP, HPRD, IntAct and MINT), plus the information from two original systematic sources of human data and from experimentally resolved 3D structures (i.e. PDBs, Protein Data Bank files, where more than two distinct proteins have been identified). Thus, APID provides PPIs reported in published research articles (with traceable PMIDs) and detected by valid experimental interaction methods that give evidences about such protein interactions (following the `ontology and controlled vocabulary': www.ebi.ac.uk/ols/ontologies/mi; developed by `HUPO PSI-MI'). Within this data mining framework, all interaction detection methods have been grouped into two main types: (i) `binary' physical direct detection methods and (ii) `indirect' methods. As a result of these redefinitions, APID provides unified protein interactomes including the specific `experimental evidences' that support each PPI, indicating whether the interactions can be considered `binary' (i.e. supported by at least one binary detection method) or not.
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