PDBe: enhanced structural data exploration to facilitate discovery
Protein Data Bank in Europe (PDBe) is a founding member of the worldwide Protein Data Bank (wwPDB), delivering open access to experimentally determined macromolecular structures. PDBe also delivers enriched annotations contributed by the PDBe-Knowledge Base (PDBe-KB) consortium. The macromolecular entry pages are the primary interface for millions of users who explore experimental structure data. Here, we describe the redesign of the PDBe entry pages that organize content into logical views, thereby improving usability and facilitating the use of structure models, driving fundamental and applied research, and supporting education. The new design introduces several enhancements, including integrated and central 3D visualization, sequence feature exploration, standardized molecular scenes, AI-driven residue-level annotations from text mining of the literature, and streamlined annotation access via refactored APIs. Importantly, researchers can now upload their own residue-level features and visualize them directly in structural context, displayed alongside PDBe-KB annotations. This functionality enables scientists to interpret unpublished or private data in relation to high-quality structural information, lowering barriers for those without prior expertise in structural biology. Together, these updates create a more accessible, flexible, and scalable framework for interacting with structural data, expanding the resource's value to both domain specialists and the wider life sciences community.
Authors
- Genevieve L. Evans (ORCID: https://orcid.org/0000-0002-8612-9539)
- Sri Devan Appasamy (ORCID: https://orcid.org/0000-0001-6609-3535)
- Weslley Morellato Bueno (ORCID: https://orcid.org/0000-0002-5109-8728)
- M. Vollmar (ORCID: https://orcid.org/0000-0002-9162-9159)
- Sreenath Sasidharan Nair (ORCID: https://orcid.org/0000-0002-6861-7627)
- Christopher J. Thorpe (ORCID: https://orcid.org/0000-0002-4341-0320)
- Grisell Díaz Leines (ORCID: https://orcid.org/0000-0002-3048-5315)
- Cristian A. Escobar (ORCID: https://orcid.org/0000-0002-4607-2996)
- Preeti Choudhary (ORCID: https://orcid.org/0000-0003-2340-3278)
- Joseph I. J. Ellaway (ORCID: https://orcid.org/0000-0002-6670-5391)
- Sameer S Velankar (ORCID: https://orcid.org/0000-0002-8439-5964)
- Romana Gáborová (ORCID: https://orcid.org/0009-0009-5900-9513)
- Radka Svobodová Vařeková (ORCID: https://orcid.org/0000-0002-3840-8760)
- Jennifer R. Fleming (ORCID: https://orcid.org/0000-0003-4016-8740)
- Marcelo Querino Lima Afonso (ORCID: https://orcid.org/0000-0002-9966-8187)
- David Sehnal (ORCID: https://orcid.org/0000-0002-0682-3089)
- Adam Midlik (ORCID: https://orcid.org/0000-0003-0455-2235)
- Ibrahim Roshan Kunnakkattu (ORCID: https://orcid.org/0000-0002-8646-0969)
- Deepti Gupta (ORCID: https://orcid.org/0000-0001-9999-5607)
- Déborah Harrus (ORCID: https://orcid.org/0000-0002-7651-672X)
- Damian Bertoni (ORCID: https://orcid.org/0000-0001-8207-2486)
- Ahsan Tanweer (ORCID: https://orcid.org/0000-0002-4793-3700)
- Maxim I. Tsenkov (ORCID: https://orcid.org/0000-0002-4870-239X)
- Ivanna Pidruchna (ORCID: https://orcid.org/0009-0001-9820-5287)
- Urmila Paramval (ORCID: https://orcid.org/0009-0001-9221-4596)
- Paulyna Magaña (ORCID: https://orcid.org/0009-0004-1524-2966)
- Adam Bellaiche (ORCID: https://orcid.org/0000-0003-2465-2313)
- Sudakshina Ganguly (ORCID: https://orcid.org/0000-0001-5452-6591)
- Dare Kayode Lawal
- Balakumaran Balasubramaniyan
- Mihai Todor (ORCID: https://orcid.org/0009-0006-4585-8790)
Institutions
- European Bioinformatics Institute (GB)
- Central European Institute of Technology (CZ)
- Masaryk University (CZ)
- Central European Institute of Technology – Masaryk University (CZ)
- Bioinformatics Institute (RU)
Publication Details
- Journal
- Nucleic Acids Research
- Published
- 2025-10-15
- DOI
- https://doi.org/10.1093/nar/gkaf1120
- Citations
- 1
- Primary Topic
- Enzyme Structure and Function
- Type
- article
- Field-Weighted Citation Impact
- 0.52