ArticleNucleic acids research2022
PDBe-KB: collaboratively defining the biological context of structural data.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers, 1 of them a synthesis that pooled it.
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Who cites it
46 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Graph databases in systems biology: a systematic review.Briefings in bioinformatics · 2024Pooled it
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- Modern resources for intrinsic disorder predictions: protein language models, deep learning, meta-servers, and databases.Cellular and molecular life sciences : CMLS · 2026Review
- Article
- DisProt in 2026: enhancing intrinsically disordered proteins accessibility, deposition, and annotation.Nucleic acids research · 2026Article
- PDBe: enhanced structural data exploration to facilitate discovery.Nucleic acids research · 2026Article
- From CASP13 to the Nobel Prize: DeepMind's AlphaFold Journey in Revolutionizing Protein Structure Prediction and Beyond.Current protein & peptide science · 2026Review
- Chart builder: an interactive tool for user driven data visualization in the electron microscopy data bank.Frontiers in bioinformatics · 2026Article
- Halogen bonds between ligands and proteins: Can we use them in validation?Protein science : a publication of the Protein Society · 2025Article
- ModelArchive: A Deposition Database for Computational Macromolecular Structural Models.Journal of molecular biology · 2025Article
- PDBCharges: Quantum-Mechanical Partial Atomic Charges for PDB Structures.Nucleic acids research · 2025Article
- MobiDB-lite 4.0: faster prediction of intrinsic protein disorder and structural compactness.Bioinformatics (Oxford, England) · 2025Article
- PDBe tools for an in-depth analysis of small molecules in the Protein Data Bank.Protein science : a publication of the Protein Society · 2025Article
- PIPENN-EMB ensemble net and protein embeddings generalise protein interface prediction beyond homology.Scientific reports · 2025Article
- Challenges in bridging the gap between protein structure prediction and functional interpretation.Proteins · 2025Article
- Performance exploration of multi-gene panels of alopecia areata susceptibility and drug-binding targets.Frontiers in physiology · 2025Article
- Comparative evaluation of methods for the prediction of protein-ligand binding sites.Journal of cheminformatics · 2024Article
- Large-scale annotation of biochemically relevant pockets and tunnels in cognate enzyme-ligand complexes.Journal of cheminformatics · 2024Article
- Multiresolution molecular dynamics simulations reveal the interplay between conformational variability and functional interactions in membrane-bound cytochrome P450 2B4.Protein science : a publication of the Protein Society · 2024Article
- Validation of electron-microscopy maps using solution small-angle X-ray scattering.Acta crystallographica. Section D, Structural biology · 2024Article
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1 author.
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Abstract
The Protein Data Bank in Europe - Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or relevant to the Protein Data Bank (PDB). The goal of PDBe-KB is to place macromolecular structure data in their biological context by developing standardised data exchange formats and integrating functional annotations from the contributing partner resources into a knowledge graph that can provide valuable biological insights. Since we described PDBe-KB in 2019, there have been significant improvements in the variety of available annotation data sets and user functionality. Here, we provide an overview of the consortium, highlighting the addition of annotations such as predicted covalent binders, phosphorylation sites, effects of mutations on the protein structure and energetic local frustration. In addition, we describe a library of reusable web-based visualisation components and introduce new features such as a bulk download data service and a novel superposition service that generates clusters of superposed protein chains weekly for the whole PDB archive.
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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.