PDBe in 2027: integrating literature annotations, molecular dynamics data, and AI-ready access

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Abstract
The Protein Data Bank in Europe (PDBe; pdbe.org) provides open access to experimentally determined biomacromolecular structures and enriches these data with biological and functional context. Here, we describe recent developments that expand the information connected to PDB structures and introduce new ways for researchers and computational tools to access it. Literature integration has been extended to additional open-access publications, substantially increasing the availability of residue-level annotations mined from the scientific literature. Cross-links to molecular dynamics simulations in MDposit have been established, and simulation-derived residue-level annotations, including relative solvent accessibility and membrane-related properties, have been integrated into PDBe-KB (pdbekb.org). PDBe entry pages now expose additional experimental and sequence information, links to related resources, and extended PDB identifiers. Protein channel, tunnel, and pore analyses generated using MOLE have also been incorporated into our weekly release pipeline and made available for download. Improved API documentation facilitates the discovery of data fields and search parameters, while three Model Context Protocol servers facilitate agentic access to the PDBe APIs, Search, and the PDBe-KB knowledge graph. Together, these developments make structural data and its wider biological context easier to discover, interpret, and reuse through both conventional and agentic workflows.
Funding Information
  • Biotechnology and Biological Sciences Research Council (BB/W017970/1)
  • Biotechnology and Biological Sciences Research Council (UKRI1876)
  • Wellcome Trust (223739/Z/21/Z)
  • Wellcome Trust (10300/Z/24/Z)
  • European Union’s Horizon Europe Programme (101094651)
  • European Union’s Horizon Europe Programme (101292906)
  • Centre of Excellence for Computational Biomolecular Research (101093290)
  • Spanish Ministry of Science (PID2024-155247NB-I00)
  • European Union’s Horizon 2020 Research and Innovation Programme
  • Marie Skłodowska-Curie (945405)
  • ARISE2 fellowship programme (101178241)
  • Czech Republic JuniorStar project (22-30571M)
  • Palacký University Olomouc Project (IGA_PrF_2026_002)
  • Ministry of Education, Youth and Sports of the Czech Republic (LM2023055)
  • ELIXIR-IMPACT (8K0208)
  • Biological Data Management and Analysis Core Facility of CEITEC Masaryk University (LM2023055)
  • European Molecular Biology Laboratory

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