ArticleProteome science2012
IDDI: integrated domain-domain interaction and protein interaction analysis system.
Article in Proteome science, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Splitpea: a Python package for protein-protein interaction network rewiring analysis due to alternative splicing.Bioinformatics (Oxford, England) · 2026Article
- PPIXpress and PPICompare webservers infer condition-specific and differential PPI networks.Bioinformatics advances · 2025Article
- Exploring Viral-Host Protein Interactions as Antiviral Therapies: A Computational Perspective.Microorganisms · 2024Review
- HuCoPIA: An Atlas of Human vs. SARS-CoV-2 Interactome and the Comparative Analysis with OtherViruses · 2023Article
- TritiKBdb: A Functional Annotation Resource for Deciphering the Complete Interaction Networks in Wheat-Karnal Bunt Pathosystem.International journal of molecular sciences · 2022Article
- Deciphering the Host-Pathogen Interactome of the Wheat-Common Bunt System: A Step towards Enhanced Resilience in Next Generation Wheat.International journal of molecular sciences · 2022Article
- Deciphering the Crosstalk Mechanisms of Wheat-Stem Rust Pathosystem: Genome-Scale Prediction Unravels Novel Host Targets.Frontiers in plant science · 2022Article
- Predicted mouse interactome and network-based interpretation of differentially expressed genes.PloS one · 2022Article
- mPPI: a database extension to visualize structural interactome in a one-to-many manner.Database : the journal of biological databases and curation · 2021Article
- HIR V2: a human interactome resource for the biological interpretation of differentially expressed genes via gene set linkage analysis.Database : the journal of biological databases and curation · 2021Article
- Detecting Rewiring Events in Protein-Protein Interaction Networks Based on Transcriptomic Data.Frontiers in bioinformatics · 2021Review
- Computational Systems Biology of Alfalfa - Bacterial Blight Host-Pathogen Interactions: Uncovering the Complex Molecular Networks for Developing Durable Disease Resistant Crop.Frontiers in plant science · 2021Article
- An Ebola,Computational and structural biotechnology journal · 2021Article
- Predicted rat interactome database and gene set linkage analysis.Database : the journal of biological databases and curation · 2020Article
- Predicted functional interactome of Caenorhabditis elegans and a web tool for the functional interpretation of differentially expressed genes.Biology direct · 2020Article
- Genome-wide inference of the Camponotus floridanus protein-protein interaction network using homologous mapping and interacting domain profile pairs.Scientific reports · 2020Article
- Predicted Drosophila Interactome Resource and web tool for functional interpretation of differentially expressed genes.Database : the journal of biological databases and curation · 2020Article
- Gain-of-Function Mutations: An Emerging Advantage for Cancer Biology.Trends in biochemical sciences · 2019Review
- Context-dependent prediction of protein complexes by SiComPre.NPJ systems biology and applications · 2018Article
- ChiPPI: a novel method for mapping chimeric protein-protein interactions uncovers selection principles of protein fusion events in cancer.Nucleic acids research · 2017Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDeciphering protein-protein interaction (PPI) in domain level enriches valuable information about binding mechanism and functional role of interacting proteins. The 3D structures of complex proteins are reliable source of domain-domain interaction (DDI) but the number of proven structures is very limited. Several resources for the computationally predicted DDI have been generated but they are scattered in various places and their prediction show erratic performances. A well-organized PPI and DDI analysis system integrating these data with fair scoring system is necessary.
methodWe integrated three structure-based DDI datasets and twenty computationally predicted DDI datasets and constructed an interaction analysis system, named IDDI, which enables to browse protein and domain interactions with their relationships. To integrate heterogeneous DDI information, a novel scoring scheme is introduced to determine the reliability of DDI by considering the prediction scores of each DDI and the confidence levels of each prediction method in the datasets, and independencies between predicted datasets. In addition, we connected this DDI information to the comprehensive PPI information and developed a unified interface for the interaction analysis exploring interaction networks at both protein and domain level.
resultIDDI provides 204,705 DDIs among total 7,351 Pfam domains in the current version. The result presents that total number of DDIs is increased eight times more than that of previous studies. Due to the increment of data, 50.4% of PPIs could be correlated with DDIs which is more than twice of previous resources. Newly designed scoring scheme outperformed the previous system in its accuracy too. User interface of IDDI system provides interactive investigation of proteins and domains in interactions with interconnected way. A specific example is presented to show the efficiency of the systems to acquire the comprehensive information of target protein with PPI and DDI relationships. IDDI is freely available at http://pcode.kaist.ac.kr/iddi/.
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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 OpenQuestion graph.