ArticleNucleic acids research2020
PDBe-KB: a community-driven resource for structural and functional annotations.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers, 1 of them a synthesis that pooled it.
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Who cites it
73 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Iron dysregulation in COVID-19 and reciprocal evolution of SARS-CoV-2: Natura nihil frustra facit.Journal of cellular biochemistry · 2022Pooled it
- PDBe-SIFTS: an open-source tool for Structure Integration with Function, Taxonomy, and Sequences, featuring improved alignment, scoring scheme, and accelerated search.bioRxiv : the preprint server for biology · 2026Article
- PDBe: enhanced structural data exploration to facilitate discovery.Nucleic acids research · 2026Article
- Pharmacophore- and QSAR-guided discovery of natural product inhibitors targeting dehydrosqualene synthase in Staphylococcus aureus.PloS one · 2026Article
- Coenzyme-protein interactions since early life.eLife · 2025Article
- Strategies for community-sourced biocuration in bioinformatics: a case study on MIBiG 4.0.Briefings in bioinformatics · 2025Article
- DARKIN: a zero-shot benchmark for phosphosite-dark kinase association using protein language models.Bioinformatics (Oxford, England) · 2025Article
- Ten rules for a structural bioinformatic analysis.PLoS computational biology · 2025Article
- GnomAD Missense Variants of Uncertain Significance: Implications for p53 Stability and Phosphorylation.International journal of molecular sciences · 2025Article
- HADDOCK3: A Modular and Versatile Platform for Integrative Modeling of Biomolecular Complexes.Journal of chemical information and modeling · 2025Article
- LIGYSIS-web: a resource for the analysis of protein-ligand binding sites.Nucleic acids research · 2025Article
- The need to implement FAIR principles in biomolecular simulations.Nature methods · 2025Article
- Regularly updated benchmark sets for statistically correct evaluations of AlphaFold applications.Briefings in bioinformatics · 2025Article
- Exploring the molecular mechanism ofHeliyon · 2025Article
- Shared interactions of six neurotropic viruses with 38 human proteins: a computational and literature-based exploration of viral interactions and hijacking of human proteins in neuropsychiatric disorders.Discover mental health · 2025Article
- Loss of correlated proteasomal subunit expression selectively promotes the 20SCommunications biology · 2025Article
- A Theoretical Study on the Efficacy and Mechanism of Combined YAP-1 and PARP-1 Inhibitors in the Treatment of Glioblastoma Multiforme Using Peruvian MacaCurrent issues in molecular biology · 2025Article
- Bioinformatics and Deep Learning Approach to Discover Food-Derived Active Ingredients for Alzheimer's Disease Therapy.Foods (Basel, Switzerland) · 2025Article
- EMICSS: added-value annotations for EMDB entries.Bioinformatics advances · 2025Article
- CryptoBench: cryptic protein-ligand binding sites dataset and benchmark.Bioinformatics (Oxford, England) · 2024Article
13 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
1 author.
Funding
Abstract
The Protein Data Bank in Europe-Knowledge Base (PDBe-KB, https://pdbe-kb.org) is a community-driven, collaborative resource for literature-derived, manually curated and computationally predicted structural and functional annotations of macromolecular structure data, contained in the Protein Data Bank (PDB). The goal of PDBe-KB is two-fold: (i) to increase the visibility and reduce the fragmentation of annotations contributed by specialist data resources, and to make these data more findable, accessible, interoperable and reusable (FAIR) and (ii) to place macromolecular structure data in their biological context, thus facilitating their use by the broader scientific community in fundamental and applied research. Here, we describe the guidelines of this collaborative effort, the current status of contributed data, and the PDBe-KB infrastructure, which includes the data exchange format, the deposition system for added value annotations, the distributable database containing the assembled data, and programmatic access endpoints. We also describe a series of novel web-pages-the PDBe-KB aggregated views of structure data-which combine information on macromolecular structures from many PDB entries. We have recently released the first set of pages in this series, which provide an overview of available structural and functional information for a protein of interest, referenced by a UniProtKB accession.
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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.