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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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HARP Analysis of cryoEM Structures in the PDB
This repository contains the results of a hierarchical atomic resolution perception (HARP) calculation on each of the cryoEM structures deposited in the Protein Data Bank (PDB) prior to January 1, 2023. Top-level group names are the PDB IDs of the structures. HDF5 group attributes for each entry are certain metadata extracted from the mmCIF files associated with each entry. HDF5 datasets within each group are indexed relative to each other (i.e., are of the same length).
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- Award ID(s):
- 2137630
- PAR ID:
- 10560633
- Publisher / Repository:
- Zenodo
- Date Published:
- Format(s):
- Medium: X
- Right(s):
- Creative Commons Attribution 4.0 International
- Sponsoring Org:
- National Science Foundation
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