🏆 Foundational Paper

Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students.

Burley Stephen K, Berman Helen M, Duarte Jose M, Feng Zukang, Flatt Justin W, Hudson Brian P, Lowe Robert, Peisach Ezra, Piehl Dennis W, Rose Yana, Sali Andrej, Sekharan Monica, Shao Chenghua, Vallat Brinda, Voigt Maria, Westbrook John D, Young Jasmine Y, Zardecki Christine

📰 Biomolecules 📅 2022 📊 103 citations
DOI PubMed 💻 GitHub

Abstract

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the United States National Science Foundation, National Institutes of Health, and Department of Energy, supports structural biologists and Protein Data Bank (PDB) data users around the world. The RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, serves as the US data center for the global PDB archive housing experimentally-determined three-dimensional (3D) structure data for biological macromolecules. As the wwPDB-designated Archive Keeper, RCSB PDB is also responsible for the security of PDB data and weekly update of the archive. RCSB PDB serves tens of thousands of data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction) annually working on all permanently inhabited continents. RCSB PDB makes PDB data available from its research-focused web portal at no charge and without usage restrictions to many millions of PDB data consumers around the globe. It also provides educators, students, and the general public with an introduction to the PDB and related training materials through its outreach and education-focused web portal. This review article describes growth of the PDB, examines evolution of experimental methods for structure determination viewed through the lens of the PDB archive, and provides a detailed accounting of PDB archival holdings and their utilization by researchers, educators, and students worldwide.

🧬 Organisms

Oryctolagus cuniculus

💻 Code & Software

ihmwg/modelcif Low Activity

mmCIF-based extension dictionary for computed structure models

🔧 Used ⭐ 24 🍴 5 📝 Shell

💾 Data Repositories

GitHub ihmwg/ModelCIF PDB 7A6A PDB 3PCQ PDB 4BZJ PDB 7ZBT PDB 1BDS PDB 1IL8 PDB 1QLO PDB 2M3B PDB 4BY9 PDB 6X63 PDB 3J07 PDB 6R8N PDB 7RPM PDB 2MJZ PDB 2K39 PDB 2KU1 PDB 6UCJ PDB 6UCK PDB 1BRD PDB 3J4G PDB 7RM5 PDB 3J7B PDB 7SKW

🏛️ Research Organizations (ROR)

Affiliated research institutions:

🏛 Rutgers, The State University of New Jersey 🏛 Rutgers Cancer Institute 🏛 University of California San Diego 🏛 San Diego Supercomputer Center 🏛 QB3 🏛 University of California, San Francisco

📊 Figures

Figure 10

Figure 10

Experimental approaches for determination of protein structures and computational methods for predicting structures both rely on open access to genomic and 3D structure data. Here, methods for determi...

Figure 1

Figure 1

Geographic distribution of PDB depositions from 1971 to mid-2022.

Figure 2

Figure 2

PDB archive metrics. ( A ). Growth 1976u20132021. ( B ). New MX, 3DEM, and NMR structures released annually (2000u20132021). ( C ). MX and 3DEM structure counts vs. resolution (u00c5). ( D ). Average ...

Figure 3

Figure 3

PDB MX structure phasing method trends vs. year of structure release from 2001u20132021 (MR: molecular replacement; MAD: multi-wavelength anomalous dispersion; SAD: single-wavelength anomalous dispers...

Figure 4

Figure 4

Box plot display of PDB MX structure resolution vs. time. The bold solid bar within each box corresponds to the median value for structures publicly released that year. (N.B.: Small numbers of extreme...

Figure 5

Figure 5

( A ). Annual average reported resolution (blue) and annual best reported resolution (orange) for 3DEM PDB structures released 2013u20132022. ( B ). Percentage of 3DEM PDB structures released per year...

Figure 6

Figure 6

Breakdown of NMR PDB structure holdings by sample type.

Figure 7

Figure 7

Phylogenetic Tree showing PDB holdings (as of mid-2022). Within each of the three branches, PDB structure totals are provided for selected organisms. N.B.: The PDB also houses 3D structures that solel...

Figure 8

Figure 8

( A ). Geographic distribution of RCSB.org users by country. ( B ). Top 10 countries with the highest percentage of users from 2019u20132021. Data from Google Analytics.

Figure 9

Figure 9

Average monthly usage of PDB-101 ( PDB101.RCSB.org , accessed on 28 August 2022) from 2019u20132021. Data from Google Analytics.

Figure images are served from the NIH/NLM PubMed Central Open Access Subset or Europe PMC; copyright remains with the publishers and authors.

🏛️ Imaging Facility

🏛️ Rutgers, The State University of New Jersey

💬 Discussion

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