ArticleBioinformatics (Oxford, England)2019
Finding enzyme cofactors in Protein Data Bank.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Coenzyme-protein interactions since early life.eLife · 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
- CIAO1 and MMS19 deficiency: A lethal neurodegenerative phenotype caused by cytosolic Fe-S cluster protein assembly disorders.Genetics in medicine : official journal of the American College of Medical Genetics · 2024Article
- PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank.Journal of cheminformatics · 2023Article
- NMR-Chemical-Shift-Driven Protocol Reveals the Cofactor-Bound, Complete Structure of Dynamic Intermediates of the Catalytic Cycle of Oncogenic KRAS G12C Protein and the Significance of the MgInternational journal of molecular sciences · 2023Article
- Accurate prediction by AlphaFold2 for ligand binding in a reductive dehalogenase and implications for PFAS (per- and polyfluoroalkyl substance) biodegradation.Scientific reports · 2023Article
- UniProt: the Universal Protein Knowledgebase in 2023.Nucleic acids research · 2023Article
- Annotation of biologically relevant ligands in UniProtKB using ChEBI.Bioinformatics (Oxford, England) · 2023Article
- PDBe and PDBe-KB: Providing high-quality, up-to-date and integrated resources of macromolecular structures to support basic and applied research and education.Protein science : a publication of the Protein Society · 2022Article
- PDBe-KB: collaboratively defining the biological context of structural data.Nucleic acids research · 2022Article
- PDBe: improved findability of macromolecular structure data in the PDB.Nucleic acids research · 2020Article
- PDBe-KB: a community-driven resource for structural and functional annotations.Nucleic acids research · 2020Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
motivationCofactors are essential for many enzyme reactions. The Protein Data Bank (PDB) contains >67 000 entries containing enzyme structures, many with bound cofactor or cofactor-like molecules. This work aims to identify and categorize these small molecules in the PDB and make it easier to find them.
resultsThe Protein Data Bank in Europe (PDBe; pdbe.org) has implemented a pipeline to identify enzyme cofactor and cofactor-like molecules, which are now part of the PDBe weekly release process. AVAILABILITY AND IMPLEMENTATION: Information is made available on the individual PDBe entry pages at pdbe.org and programmatically through the PDBe REST API (pdbe.org/api). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.