PDBe: improved findability of macromolecular structure data in the PDB

By David R. Armstrong, J. Berrisford, M. J. Conroy, A. Gutmanas, S. Anyango, Preeti Choudhary, Alice R. Clark, J. M. Dana, M. Deshpande, Roisin Dunlop and 21 more. 2019

178 citations recorded by the source corpus.

Abstract The Protein Data Bank in Europe (PDBe), a founding member of the Worldwide Protein Data Bank (wwPDB), actively participates in the deposition, curation, validation, archiving and dissemination of macromolecular structure data. PDBe supports diverse research communities in their use of macromolecular structures by enriching the PDB data and by providing advanced tools and services for effective data access, visualization and analysis. This paper details the enrichment of data at PDBe, including mapping of RNA structures to Rfam, and identification of molecules that act as cofactors. PDBe has developed an advanced search facility with ∼100 data categories and sequence searches. New features have been included in the LiteMol viewer at PDBe, with updated visualization of carbohydrates and nucleic acids. Small molecules are now mapped more extensively to external databases and their visual representation has been enhanced. These advances help users to more easily find and interpret macromolecular structure data in order to solve scientific problems.

Subfields: Materials Chemistry, Molecular Biology, Spectroscopy

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Citations in the corpus

GPCRdb in 2021: integrating GPCR sequence, structure and function (2020, methodology): “The Structure Constructs section in GPCRdb integrates GPCR structure sequence from PDB, residue annotations from SIFTS (35) and an extensive manual literature annotation of mutation effects and inserts (e.g. purification tags) as well as experimental methods and reagents for GPCR structure determina”
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models (2021, background): “Although recent advances in the field of electron cryo-microscopy and hybrid and integrative methods (I / HM) for structure determination have accelerated the pace of structure determination, the gap between known protein sequences and experimental protein structures continues to expand (6,8).”
The ProteomeXchange consortium at 10 years: 2023 update (2022, unknown): “In the context of data archiving activities, in addition to the already-covered topic of sensitive proteomics datasets, improved support will be provided for structural proteomics datasets, including linking submissions of different structural data to the Protein Data Bank (PDB) (61).”
InterPro: the protein sequence classification resource in 2025 (2024, unknown): “Ad-ditionally, InterPro data are integral to various annotation pipelines, including Ensembl ( 28 ), Ensembl Genomes ( 29 ), PDBe ( 30 ), Blast2GO ( 31 ), Genome Properties ( 32 ), MGnify ( 33 ) and MGnify Genomes ( 34 ).”
Rfam 14: expanded coverage of metagenomic, viral and microRNA families (2020, methodology): “For example, PDBe uses Rfam to enable searching for RNA chains, such as tRNA or rRNA, in 3D structures (9), while RNAcentral uses Rfam to detect incomplete sequences, RNA type annotations errors, and provide other quality controls (10).”
SwissDock 2024: major enhancements for small-molecule docking with Attracting Cavities and AutoDock Vina (2024, background): “…such as ChEBI ( 24 ) and the chemical component dictionary from the world-wide Protein Data Bank ( 25 ,26 ) for ligands, as well as PDBe ( 27 ), the AlphaFold protein structure database ( 28 ) or SWISS-MODEL ( 29 ) for targets, providing easy access to a wealth of high-quality structural…”
RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning (2022, background): “org, (54)); Protein Data Bank Japan (PDBj, PDBj.”
The EMBL-EBI Job Dispatcher sequence analysis tools framework in 2024 (2024, methodology): “Sequence dataset updates and releases are routinely deployed for datasets such as UniProt, PDBe ( 19 ), Ensembl Genomes, WormBase Parasite ( 20 ), and ENA.”
UniProt: the Universal Protein Knowledgebase in 2023 (2022, background): “…the chemical ontology ChEBI (8), focusing on biologically relevant (or ‘cognate’) ligands such as activators, inhibitors, and cofactors and their corresponding binding sites, knowledge of which is captured from the literature and protein structures in the Protein Data Bank (PDB / PDBe) (9,10).”
PDBe-KB: collaboratively defining the biological context of structural data (2021, background): “To date, the PDB contains over 180 000 structures of 55 000 distinct proteins, with around 12 000 new PDB entries deposited annually (7).”