RCSB Protein Data Bank: Delivering integrative structures alongside experimental structures and computed structure models
The Protein Data Bank (PDB) archives 3D structures of macromolecules determined experimentally using various methods. It is jointly managed by the Worldwide Protein Data Bank (wwPDB) consortium. Research Collaboratory for Structural Bioinformatics (RCSB) PDB, the US data center for the PDB, provides streamlined access to >240 000 structures through a variety of research-focused tools on RCSB.org. In addition, RCSB.org makes available over 1 million computed structure models (CSMs) predicted using deep learning methods and archived in the AlphaFold Database and ModelArchive. The PDB-IHM system was developed as a wwPDB project based on community recommendations to archive structures determined using integrative/hybrid methods (IHM). These structures are computed by combining information from multiple experimental and computational techniques to overcome the limitations of traditional single methods (e.g. macromolecular crystallography, 3D electron microscopy, nuclear magnetic resonance spectroscopy). In 2024, PDB-IHM was unified with the PDB to archive integrative structures alongside single-method experimental structures. These integrative structures have been made accessible via the RCSB.org website, facilitating efficient delivery of IHM data to a broad community of PDB users. Herein, we describe the expanded capabilities of RCSB.org that support discovery, analysis, and visualization of integrative structures together with single-method experimental structures and CSMs.
Authors
- Charmi Bhikadiya (ORCID: https://orcid.org/0000-0002-1587-5139)
- Ezra Peisach (ORCID: https://orcid.org/0000-0002-7905-6327)
- José M. Duarte (ORCID: https://orcid.org/0000-0002-9544-5621)
- Jasmine Y. Young (ORCID: https://orcid.org/0000-0001-8896-6878)
- Joan Segura (ORCID: https://orcid.org/0000-0001-5593-735X)
- Arthur O. Zalevsky (ORCID: https://orcid.org/0000-0001-6987-8119)
- Benjamin Webb (ORCID: https://orcid.org/0000-0003-3360-4540)
- Henry Chao
- Sebastian Bittrich (ORCID: https://orcid.org/0000-0003-3576-0387)
- Andrej Săli (ORCID: https://orcid.org/0000-0003-0435-6197)
- Jared Sagendorf (ORCID: https://orcid.org/0009-0009-1195-1753)
- Vladimir Guranović (ORCID: https://orcid.org/0000-0001-7648-4628)
- Alexander Rose (ORCID: https://orcid.org/0000-0002-0893-5551)
- Chunxiao Bi
- Brinda Vallat (ORCID: https://orcid.org/0000-0002-4076-8984)
- David W. Raymond
- Yana Rose (ORCID: https://orcid.org/0000-0003-1018-5718)
- Maria Voigt (ORCID: https://orcid.org/0000-0003-3103-7781)
- S.K. Burley (ORCID: https://orcid.org/0000-0002-2487-9713)
- Helen M. Berman (ORCID: https://orcid.org/0000-0002-3337-0660)
- Jeremy Henry
- Monica R. Sekharan (ORCID: https://orcid.org/0000-0002-2694-7003)
- James M. Smith (ORCID: https://orcid.org/0000-0002-7465-6067)
- Zukang Feng (ORCID: https://orcid.org/0000-0002-1788-6579)
- Dennis W. Piehl
- Aditya Pingale
Institutions
- Rutgers, The State University of New Jersey (US)
- QB3 (US)
- University of Southern California (US)
- San Diego Supercomputer Center (US)
- Biologie Computationnelle, Quantitative et Synthétique (FR)
- Clinical Research Consortium (US)
Publication Details
- Journal
- Nucleic Acids Research
- Published
- 2025-11-08
- DOI
- https://doi.org/10.1093/nar/gkaf1187
- Citations
- 3
- Primary Topic
- Enzyme Structure and Function
- Type
- article
- Field-Weighted Citation Impact
- 1.55