ArticleNucleic acids research2014
IDEAL in 2014 illustrates interaction networks composed of intrinsically disordered proteins and their binding partners.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers, 1 of them a synthesis that pooled it.
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Who cites it
68 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Comprehensive analysis of regulated cell death pathways: intrinsic disorder, protein-protein interactions, and cross-pathway communication.Apoptosis : an international journal on programmed cell death · 2025Pooled it
- Beyond the structure-function paradigm: A comprehensive review of intrinsically disordered proteins.Biochemistry and biophysics reports · 2026Review
- Predicting molecular recognition features in protein sequences with MoRFchibi 2.0.BMC bioinformatics · 2026Article
- Modern resources for intrinsic disorder predictions: protein language models, deep learning, meta-servers, and databases.Cellular and molecular life sciences : CMLS · 2026Review
- Expose flexible conformations for intrinsically disordered protein.Current research in structural biology · 2025Article
- A deep learning method for predicting interactions for intrinsically disordered regions of proteins.bioRxiv : the preprint server for biology · 2025Article
- DARUMA: a gateway to fast and easy prediction of intrinsically disordered regions.PeerJ. Computer science · 2025Article
- Evaluation of predictions of disordered binding regions in the CAID2 experiment.Computational and structural biotechnology journal · 2025Review
- Systematic discovery of DNA-binding tandem repeat proteins.Nucleic acids research · 2024Article
- StrIDR: a database of intrinsically disordered regions of proteins with experimentally resolved structures.bioRxiv : the preprint server for biology · 2024Article
- Protein embeddings predict binding residues in disordered regions.Scientific reports · 2024Article
- Advanced computational approaches to understand protein aggregation.Biophysics reviews · 2024Review
- PED in 2024: improving the community deposition of structural ensembles for intrinsically disordered proteins.Nucleic acids research · 2024Article
- Prediction of folding patterns for intrinsic disordered protein.Scientific reports · 2023Article
- Tutorial: a guide for the selection of fast and accurate computational tools for the prediction of intrinsic disorder in proteins.Nature protocols · 2023Review
- Minimum information guidelines for experiments structurally characterizing intrinsically disordered protein regions.Nature methods · 2023Review
- Biophysical and Integrative Characterization of Protein Intrinsic Disorder as a Prime Target for Drug Discovery.Biomolecules · 2023Review
- Computational Prediction of Protein Intrinsically Disordered Region Related Interactions and Functions.Genes · 2023Review
- How AlphaFold2 Predicts Conditionally Folding Regions Annotated in an Intrinsically Disordered Protein Database, IDEAL.Biology · 2023Article
- MobiDB: 10 years of intrinsically disordered proteins.Nucleic acids research · 2023Article
8 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
IDEAL (Intrinsically Disordered proteins with Extensive Annotations and Literature, http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/) is a collection of intrinsically disordered proteins (IDPs) that cannot adopt stable globular structures under physiological conditions. Since its previous publication in 2012, the number of entries in IDEAL has almost tripled (120 to 340). In addition to the increase in quantity, the quality of IDEAL has been significantly improved. The new IDEAL incorporates the interactions of IDPs and their binding partners more explicitly, and illustrates the protein-protein interaction (PPI) networks and the structures of protein complexes. Redundant experimental data are arranged based on the clustering of Protein Data Bank entries, and similar sequences with the same binding mode are grouped. As a result, the new IDEAL presents more concise and informative experimental data. Nuclear magnetic resonance (NMR) disorder is annotated in a systematic manner, by identifying the regions with large deviations among the NMR models. The ordered/disordered and new domain predictions by DICHOT are available, as well as the domain assignments by HMMER. Some examples of the PPI networks and the highly deviated regions derived from NMR models will be described, together with other advances. These enhancements will facilitate deeper understanding of IDPs, in terms of their flexibility, plasticity and promiscuity.
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