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Abstract 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.
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This content will become publicly available on August 1, 2026
PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures
Structures of many large biomolecular assemblies are now being determined using integrative approaches. In these approaches, information derived from multiple experimental and computational methods is combined to compute three-dimensional structures of multi-protein complexes and other macromolecular machines. A standalone prototype data resource for integrative structures called PDB-Dev was built, based on recommendations of the Integrative and Hybrid Methods (IHM) Task Force of the Worldwide Protein Data Bank (wwPDB). This effort included developing data standards and software tools for collecting, curating, validating, visualizing, archiving, and disseminating integrative structures that span diverse spatiotemporal scales and conformational states. Mechanisms have been created to validate integrative structures based on the experimental data underpinning them. Building upon this foundational framework, PDB-Dev has been further expanded to handle large dynamic macromolecular systems and integrative structures that combine, for example, experimental restraints with atomic coordinates computed by machine learning algorithms. Data standards and supporting tools have also been extended to capture information about biomolecular dynamics, such as conformational transitions and related kinetic data derived from biophysical methods. Recently, PDB-Dev was unified with the PDB archive and rebranded as PDB-IHM (pdb-ihm.org), further promoting FAIR (Findable, Accessible, Interoperable, and Reusable) principles of data stewardship for integrative structural biology.
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- Award ID(s):
- 2112966
- PAR ID:
- 10653055
- Publisher / Repository:
- Journal of Molecular Biology, Elsevier
- Date Published:
- Journal Name:
- Journal of Molecular Biology
- Volume:
- 437
- Issue:
- 15
- ISSN:
- 0022-2836
- Page Range / eLocation ID:
- 168963
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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