PDBe

PDBe
Name	Protein Data Bank in Europe
Acronym	PDBe
Established	1996
Type	Bioinformatics resource
Location	Europe
Parent organization	European Bioinformatics Institute

PDBe is a European archival and annotation resource for macromolecular structure data that serves structural biologists, bioinformaticians, and chemists. It collects, curates, and disseminates three-dimensional coordinates, experimental data, and derived annotations for proteins, nucleic acids, and complexes, integrating with major international repositories and scientific infrastructures. PDBe supports research across structural biology, drug discovery, and molecular medicine by providing standardized access to data produced by laboratories, beamlines, and consortia.

Overview

PDBe operates as a regional partner within the Worldwide Protein Data Bank framework alongside RCSB PDB, PDBj, and BMRB. It receives atomic models from experimental facilities such as European Synchrotron Radiation Facility, Diamond Light Source, and Swiss Light Source, and from research groups at institutions like Max Planck Institute, University of Cambridge, University of Oxford, and CNRS. PDBe integrates metadata cross-references to resources including UniProt, Gene Ontology, Pfam, SCOPe, CATH, InterPro, ChEMBL, DrugBank, Ensembl, RefSeq, KEGG, Reactome, BioModels, IntAct, STRING, Europe PMC, PubMed, EMBL-EBI, Wellcome Sanger Institute, Institut Pasteur, Harvard Medical School, Massachusetts Institute of Technology, Stanford University, Yale University, Imperial College London, Karolinska Institutet, ETH Zurich, University of California, San Francisco, Broad Institute, Johns Hopkins University, Cold Spring Harbor Laboratory, Weizmann Institute of Science, University of Tokyo, Seoul National University, Monash University, University of Melbourne, University of Toronto, McGill University, University of Chicago, Princeton University, Columbia University, University of Pennsylvania, University of California, Berkeley, California Institute of Technology, National Institute of Standards and Technology, European Molecular Biology Laboratory, Wellcome Trust, European Union, Human Frontier Science Program, Howard Hughes Medical Institute.

History

The initiative began in the context of global efforts exemplified by the original Protein Data Bank collaboration and the creation of regional partners such as RCSB PDB and PDBj. PDBe developed at the European Bioinformatics Institute within the European Molecular Biology Laboratory to serve European structural biology communities including groups at Max Planck Institute for Biochemistry and Institut Pasteur. Over time PDBe adopted community standards promulgated by organizations like the Worldwide Protein Data Bank and worked with experimental networks such as the Structural Biology Grid and synchrotron consortia. Major milestones include integration with cryo-electron microscopy initiatives linked to Electron Microscopy Data Bank developments and alignment with annotation projects active at UniProt Consortium, GO Consortium, and FAIR principles advocates.

Data and Services

PDBe archives experimentally determined atomic coordinates, electron density maps, cryo-EM reconstructions, and NMR restraints from depositors at laboratories such as Scripps Research Institute and Riken. It provides search and retrieval services interoperable with portals like ELIXIR, EBI Search, and OmicsDI. PDBe annotates entries with cross-references to databases including UniProtKB, Ensembl Genomes, Pfam, InterProScan, SCOP, CATH-Gene3D, MEROPS, PROSITE, ConSurf, PISA, PDBePISA (note: tool name not linked here), PDBeFold, PDBePISA Archive and links to literature in PubMed Central, Europe PMC, CrossRef, ORCID records for depositors at institutions like University College London and Trinity College Dublin. PDBe supports programmatic access via APIs used by projects at Google DeepMind, AlphaFold Protein Structure Database collaborations, and computational pipelines in groups at Rosalind Franklin Institute.

Structure Annotation and Standards

PDBe applies community standards developed by the wwPDB Validation Task Force, the International Union of Crystallography, and cross-disciplinary initiatives such as the FAIRsharing registry. Annotation schemes link structural features to entries in UniProt, Gene Ontology Consortium, Pfam Consortium, and CATH, and employ nomenclature standards from IUPAC and recommendation sets from PDBx/mmCIF governance. Validation reports reference criteria used by Acta Crystallographica Section D reviewers and experimental metadata standards advocated by FAIR principles and MIABIS-style initiatives. PDBe curators interact with depositors from laboratories including MRC Laboratory of Molecular Biology and European Molecular Biology Organization members to ensure compliance with community deposition policies.

Tools and Resources

PDBe develops visualization and analysis tools used by researchers at University of Cambridge Department of Chemistry, ETH Zurich Institute of Biochemistry, and biotechnology companies like GlaxoSmithKline and AstraZeneca. Interactive viewers, mapping services, and RESTful APIs enable integration with computational suites such as PyMOL, UCSF Chimera, Rosetta, Phenix, CCP4, GROMACS, AutoDock, HADDOCK, MODELLER, Clustal Omega, MAFFT, BLAST, HHpred, PSIPRED, DALI, VMD, Coot, ISOLDE, ISMB-related workflows, and cloud platforms used by Amazon Web Services and Google Cloud Platform. PDBe resources underpin educational initiatives at institutions like Cold Spring Harbor Laboratory and courses at European Molecular Biology Laboratory practical schools.

Collaborations and Governance

PDBe participates in governance structures coordinated by the Worldwide Protein Data Bank partnership and engages with funders such as the Wellcome Trust, the European Commission, and national research councils including UK Research and Innovation. Collaborative networks include ELIXIR, EMBL-EBI service teams, and methodological consortia involving CryoEM Grid beamline consortia and community groups at ISMB, Gordon Research Conferences, Cold Spring Harbor Conferences, and Biophysical Society meetings. Advisory input is received from domain experts affiliated with Max Planck Society, Karolinska Institutet, Harvard Medical School, and industrial partners like Novartis and Pfizer.

Category:Bioinformatics