ArticleNucleic acids research2021
PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers.
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Who cites it
74 citing papers in PubMed.
- In Search of Shape in the Unshaped: Constructing Ensembles of Intrinsically Disordered Proteins.Biophysics reviews · 2026Article
- Atomic resolution ensembles of intrinsically disordered proteins with Alphafold.Nature communications · 2026Article
- Constraint Decoupled Latent Diffusion for Protein Backmapping.Journal of chemical theory and computation · 2026Article
- Molecular grammars of predicted intrinsically disordered regions that span the human proteome.Cell · 2026Article
- Exploring Novel E3 Ligases and Neosubstrates for Molecular Glue Degraders and Therapeutic Applications in Cancer.Oncology research · 2026Review
- Accurate Generation of Conformational Ensembles for Intrinsically Disordered Proteins with IDPFold.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Structure and Function of the Extracellular Matrix in Normal and Pathological Conditions: Looking at the Bicuspid Aortic Valve.International journal of molecular sciences · 2025Review
- DSSP 4: FAIR annotation of protein secondary structure.Protein science : a publication of the Protein Society · 2025Article
- Structural and Functional Relevance of Charge-Based Transient Interactions inside Intrinsically Disordered Proteins.ACS physical chemistry Au · 2025Article
- Structural plasticity of the FOXO-DBD:p53-TAD interaction.Nature communications · 2025Article
- Noncovalent Lasso Entanglements are Common in Experimentally Derived Intrinsically Disordered Protein Ensembles and Strongly Influenced by Protein Length and Charge.The journal of physical chemistry. B · 2025Article
- AlphaFold prediction of structural ensembles of disordered proteins.Nature communications · 2025Article
- Dissecting Henipavirus W proteins conformational and fibrillation properties: contribution of their N- and C-terminal constituent domains.The FEBS journal · 2025Article
- Challenges in bridging the gap between protein structure prediction and functional interpretation.Proteins · 2025Article
- Structural and Functional Relevance of Charge Based Transient Interactions inside Intrinsically Disordered Proteins.bioRxiv : the preprint server for biology · 2024Article
- Data-driven probabilistic definition of the low energy conformational states of protein residues.NAR genomics and bioinformatics · 2024Article
- Design of intrinsically disordered protein variants with diverse structural properties.Science advances · 2024Article
- A curated rotamer library for common post-translational modifications of proteins.Bioinformatics (Oxford, England) · 2024Article
- Identification of Mulberrofuran as a potent inhibitor of hepatitis A virus 3CMolecular diversity · 2024Article
- Advanced computational approaches to understand protein aggregation.Biophysics reviews · 2024Review
14 more citing papers are in PubMed but not listed here.
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Authors and funding
40 authors.
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Abstract
The Protein Ensemble Database (PED) (https://proteinensemble.org), which holds structural ensembles of intrinsically disordered proteins (IDPs), has been significantly updated and upgraded since its last release in 2016. The new version, PED 4.0, has been completely redesigned and reimplemented with cutting-edge technology and now holds about six times more data (162 versus 24 entries and 242 versus 60 structural ensembles) and a broader representation of state of the art ensemble generation methods than the previous version. The database has a completely renewed graphical interface with an interactive feature viewer for region-based annotations, and provides a series of descriptors of the qualitative and quantitative properties of the ensembles. High quality of the data is guaranteed by a new submission process, which combines both automatic and manual evaluation steps. A team of biocurators integrate structured metadata describing the ensemble generation methodology, experimental constraints and conditions. A new search engine allows the user to build advanced queries and search all entry fields including cross-references to IDP-related resources such as DisProt, MobiDB, BMRB and SASBDB. We expect that the renewed PED will be useful for researchers interested in the atomic-level understanding of IDP function, and promote the rational, structure-based design of IDP-targeting drugs.
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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.