PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology

Westbrook, John D.; Young, Jasmine; Shao, Chenghua; Feng, Zhang; Guranovic, Vladimir; Lawson, Catherine L.; Vallat, Brinda; Adams, Paul D.; Berrisford, John M.; Bricogne, G.; Diederichs, Kay; Joosten, Robbie P.; Keller, Peter M.; Moriarty, Nigel W.; Sobolev, Oleg; Velankar, Sameer; Vonrhein, Clemens; Kurisu, Genji; Berman, Helen M.; Burley, S.K.; Peisach, Ezra

doi:10.1016/j.jmb.2022.167599

Cited by 58 publications

(48 citation statements)

References 56 publications

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“…PDBx/mmCIF Data Standard: PDB data architecture is defined by the PDBx/mmCIF dictionary. 56 , 57 , 58 It is the macromolecular extension of an earlier community data standard, the Crystallization Information Framework 59 ( cif.iucr.org ), developed by the International Union of Crystallography for small molecule X‐ray diffraction. The macromolecular data standard is maintained by the wwPDB partners in collaboration with wwPDB PDBx/mmCIF Working Group domain experts ( wwpdb.org/task/mmcif ).…”

Section: Resultsmentioning

confidence: 99%

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RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D

Burley

Bhikadiya

et al. 2022

Protein Science

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Now in its 52nd year of continuous operations, the Protein Data Bank (PDB) is the premiere open‐access global archive housing three‐dimensional (3D) biomolecular structure data. It is jointly managed by the Worldwide Protein Data Bank (wwPDB) partnership. The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is funded by the National Science Foundation, National Institutes of Health, and US Department of Energy and serves as the US data center for the wwPDB. RCSB PDB is also responsible for the security of PDB data in its role as wwPDB‐designated Archive Keeper. Every year, RCSB PDB serves tens of thousands of depositors of 3D macromolecular structure data (coming from macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro‐electron diffraction). The RCSB PDB research‐focused web portal (http://RCSB.org) makes PDB data available at no charge and without usage restrictions to many millions of PDB data consumers around the world. The RCSB PDB training, outreach, and education web portal (http://PDB101.RCSB.org) serves nearly 700 K educators, students, and members of the public worldwide. This invited Tools Issue contribution describes how RCSB PDB (i) is organized; (ii) works with wwPDB partners to process new depositions; (iii) serves as the wwPDB‐designated Archive Keeper; (iv) enables exploration and 3D visualization of PDB data via http://RCSB.org; and (v) supports training, outreach, and education via http://PDB101.RCSB.org. New tools and features at http://RCSB.org are presented using examples drawn from high‐resolution structural studies of proteins relevant to treatment of human cancers by targeting immune checkpoints.

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Section: Resultsmentioning

confidence: 99%

“…PDBx/mmCIF Data Standard: PDB data architecture is defined by the PDBx/mmCIF dictionary 56–58 . It is the macromolecular extension of an earlier community data standard, the Crystallization Information Framework 59 (http://cif.iucr.org), developed by the International Union of Crystallography for small molecule X‐ray diffraction.…”

Section: Resultsmentioning

confidence: 99%

RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D

Burley

Bhikadiya

et al. 2022

Protein Science

Self Cite

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“…The PDB data standard is defined by the PDBx/mmCIF dictionary [ 109 , 110 , 111 ]. It is the macromolecular extension of an earlier community data standard, the Crystallization Information Framework ( , accessed on 28 August 2022), developed for small molecules by the International Union of Crystallography [ 112 ].…”

Section: Resultsmentioning

confidence: 99%

“…It is the macromolecular extension of an earlier community data standard, the Crystallization Information Framework ( , accessed on 28 August 2022), developed for small molecules by the International Union of Crystallography [ 112 ]. The macromolecular data standard is maintained by the wwPDB partnership together with the wwPDB PDBx/mmCIF Working Group ( , accessed on 28 August 2022) [ 111 ]. wwPDB partners and the Working Group collaborate on developing terminologies for new and rapidly evolving methodologies and remediating (or enhancing) representations for existing data content.…”

Section: Resultsmentioning

confidence: 99%

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

et al. 2022

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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 RCSB.org 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, PDB101.RCSB.org. 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.

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“…PDB is a testament to how adherence to the FAIR practices can benefit both the scientific and broader communities. By defining and implementing fully machine-readable data standards, PDBx/mmCIF has been adopted by the biostructure community, making experimental 3D structure data public domain and interoperable using data exchange APIs ( 90 , 91 ). Making all the information open access and available without limitations on data usage, even for commercial users, has facilitated the discovery and development of many small-molecule and biological drugs ( 92 ).…”

Section: Building a New Data-driven Biological Culture And Automation...mentioning

confidence: 99%

A roadmap for the functional annotation of protein families: a community perspective

et al. 2022

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Over the last 25 years, biology has entered the genomic era and is becoming a science of ‘big data’. Most interpretations of genomic analyses rely on accurate functional annotations of the proteins encoded by more than 500 000 genomes sequenced to date. By different estimates, only half the predicted sequenced proteins carry an accurate functional annotation, and this percentage varies drastically between different organismal lineages. Such a large gap in knowledge hampers all aspects of biological enterprise and, thereby, is standing in the way of genomic biology reaching its full potential. A brainstorming meeting to address this issue funded by the National Science Foundation was held during 3–4 February 2022. Bringing together data scientists, biocurators, computational biologists and experimentalists within the same venue allowed for a comprehensive assessment of the current state of functional annotations of protein families. Further, major issues that were obstructing the field were identified and discussed, which ultimately allowed for the proposal of solutions on how to move forward.

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PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology

Cited by 58 publications

References 56 publications

RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D

RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D

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

A roadmap for the functional annotation of protein families: a community perspective

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