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PDBx/mmCIF Format Mandatory for Protein Data Bank Deposition

Gert-Jan BEKKER, Takahiro KUDOU, Yasuyo IKEGAWA, Reiko YAMASHITA, Genji KURISU
2019 Nihon Kessho Gakkaishi  
Gert-Jan BEKKER, Takahiro KUDOU, Yasuyo IKEGAWA, Reiko YAMASHITA and Genji KURISU: PDBx/mmCIF Format Mandatory for Protein Data Bank Deposition 2018 年 11 月 2 日,英国 Cambridge の Madingley Hall に おいて開催された  ... 
doi:10.5940/jcrsj.61.159 fatcat:sfp7xwqddvh6vpvk4o4wqxojya

Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures

Akira R. Kinjo, Gert-Jan Bekker, Hirofumi Suzuki, Yuko Tsuchiya, Takeshi Kawabata, Yasuyo Ikegawa, Haruki Nakamura
2016 Nucleic Acids Research  
The Protein Data Bank Japan (PDBj,, a member of the worldwide Protein Data Bank (ww-PDB), accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins. We herein outline the updated web user interfaces together with RESTful web services and the backend relational
more » ... base that support the former. To enhance the interoperability of the PDB data, we have previously developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, which is now a wwPDB standard called wwPDB/RDF. We have enhanced the connectivity of the wwPDB/RDF data by incorporating various external data resources. Services for searching, comparing and analyzing the ever-increasing large structures determined by hybrid methods are also described.
doi:10.1093/nar/gkw962 pmid:27789697 pmcid:PMC5210648 fatcat:pan6qdrpe5bknfgkot6blgnp6u

The life and times of the PDB format – looking towards the future with mmCIF

Gregg Crichlow, Catherine Lawson, John Westbrook, Stephen Burley, Sanja Abbott, Kumaran Baskaran, John Berrisford, Zukang Feng, Yasuyo Ikegawa, Masashi Yokochi, Jasmine Y. Young, Jeffrey Hoch (+1 others)
2021 Acta Crystallographica Section A: Foundations and Advances  
doi:10.1107/s0108767321098068 fatcat:bjkhzjzsm5hojhv6ovbgaziowa

Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB)

Paul D. Adams, Pavel V. Afonine, Kumaran Baskaran, Helen M. Berman, John Berrisford, Gerard Bricogne, David G. Brown, Stephen K. Burley, Minyu Chen, Zukang Feng, Claus Flensburg, Aleksandras Gutmanas (+23 others)
2019 Acta Crystallographica Section D: Structural Biology  
doi:10.1107/s2059798319004522 pmid:30988261 pmcid:PMC6465986 fatcat:lfqllnbmuzapnc4cv2r4za3ncy

OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive

Jasmine Y. Young, John D. Westbrook, Zukang Feng, Raul Sala, Ezra Peisach, Thomas J. Oldfield, Sanchayita Sen, Aleksandras Gutmanas, David R. Armstrong, John M. Berrisford, Li Chen, Minyu Chen (+37 others)
2017 Structure  
OneDep, a unified system for deposition, biocuration, and validation of experimentally determined structures of biological macromolecules to the PDB archive, has been developed as a global collaboration by the worldwide PDB (wwPDB) partners. This new system was designed to ensure that the wwPDB could meet the evolving archiving requirements of the scientific community over the coming decades. OneDep unifies deposition, biocuration, and validation pipelines across all wwPDB, EMDB, and BMRB
more » ... tion sites with improved focus on data quality and completeness in these archives, while supporting growth in the number of depositions and increases in their average size and complexity. In this paper, we describe the design, functional operation, and supporting infrastructure of the OneDep system, and provide initial performance assessments.
doi:10.1016/j.str.2017.01.004 pmid:28190782 pmcid:PMC5360273 fatcat:okamctypwvdrxfomgjio4rsvma

Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data

Jasmine Y Young, John D Westbrook, Zukang Feng, Ezra Peisach, Irina Persikova, Raul Sala, Sanchayita Sen, John M Berrisford, G Jawahar Swaminathan, Thomas J Oldfield, Aleksandras Gutmanas, Reiko Igarashi (+39 others)
2018 Database: The Journal of Biological Databases and Curation  
Citation details: Young,J.Y., Westbrook,J.D., Feng,Z. et al. Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data. Abstract The Protein Data Bank (PDB) is the single global repository for experimentally determined 3D structures of biological macromolecules and their complexes with ligands. The V C The Author(s) worldwide PDB (wwPDB) is the international collaboration that manages the PDB archive according to the FAIR principles: Findability,
more » ... ccessibility, Interoperability and Reusability. The wwPDB recently developed OneDep, a unified tool for deposition, validation and biocuration of structures of biological macromolecules. All data deposited to the PDB undergo critical review by wwPDB Biocurators. This article outlines the importance of biocuration for structural biology data deposited to the PDB and describes wwPDB biocuration processes and the role of expert Biocurators in sustaining a highquality archive. Structural data submitted to the PDB are examined for self-consistency, standardized using controlled vocabularies, cross-referenced with other biological data resources and validated for scientific/technical accuracy. We illustrate how biocuration is integral to PDB data archiving, as it facilitates accurate, consistent and comprehensive representation of biological structure data, allowing efficient and effective usage by research scientists, educators, students and the curious public worldwide. Database URL:
doi:10.1093/database/bay002 pmid:29688351 pmcid:PMC5804564 fatcat:pymncvy65zghjgdhleavnz7oce


2019 Nihon Kessho Gakkaishi  
IKEGAWA, Reiko YAMASHITA and Genji KURISU‥ 159 Exploring the World's Synchrotron Facilities 3.  ...  Precise Diffraction-Experiments at High-Temperatures ••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••••Nobuo ISHIZAWA‥ 181 Takahiro KUDOU, Yasuyo  ... 
doi:10.5940/jcrsj.61.index3 fatcat:zas3zekpynea5mb6hyn7vpslsu

Protein Data Bank: the single global archive for 3D macromolecular structure data

Stephen K Burley, Helen M Berman, Charmi Bhikadiya, Chunxiao Bi, Li Chen, Luigi Di Costanzo, Cole Christie, Jose M Duarte, Shuchismita Dutta, Zukang Feng, Sutapa Ghosh, David S Goodsell (+70 others)
2018 Nucleic Acids Research  
The Protein Data Bank (PDB) is the single global archive of experimentally determined three-dimensional (3D) structure data of biological macromolecules. Since 2003, the PDB has been managed by the Worldwide Protein Data Bank (wwPDB;, an international consortium that collaboratively oversees deposition, validation, biocuration, and open access dissemination of 3D macromolecular structure data. The PDB Core Archive houses 3D atomic coordinates of more than 144 000 structural models of
more » ... proteins, DNA/RNA, and their complexes with metals and small molecules and related experimental data and metadata. Structure and experimental data/metadata are also stored in the PDB Core Archive using the readily extensible wwPDB PDBx/mmCIF master data format, which will continue to evolve as data/metadata from new experimental techniques and structure determination methods are incorporated by the wwPDB. Impacts of the recently developed universal wwPDB OneDep deposition/validation/biocuration system and various methods-specific wwPDB Validation Task Forces on improving the quality of structures and data housed in the PDB Core Archive are described together with current challenges and future plans.
doi:10.1093/nar/gky949 pmid:30357364 pmcid:PMC6324056 fatcat:ca3xenxsdzgvnb7vcwi2gtomoa

Young Scientist Award Secondary Examination Developmental Engineering Breeding / Strain Development Management / Welfare Mitochondria Virus Bacteria Gene Function QTL Analysis Bioresource and Database Animal Models for Human Disease Neuroscience / Behavior Cancer Immunology Pathogenic Analysis Fertilization / Early Development

2011 Experimental animals  
Lab Anim Facility, Jikei Univ, 2 RIKEN CGM, 3 RIKEN BRC Tatsuya Furuichi 1,2 , Hiroshi Masuya -, Tomohiro -uzuki -, Kiyoshi Ohkawa 1 , -higeharu Wakana -, Shiro Ikegawa 2 1 Tamio Furuse 1 , Ikuko  ...  basement membrane disintegration at optic fissure causes mild ocular coloboma in FLS mice. 3O-74 Safety of Cell Transplantation Evaluated by MRI with SPIO-Labeled Cell tracking in Cynomolgus Monkey Yasuyo  ... 
doi:10.1538/expanim.60.234 fatcat:yuvaixnbpzgsxj6t5jyqld6ave

Management / Ethics / Welfare Genetics / Breeding / Gene Function Bioresource Developmental Engineering / Regenerative Therapy Infectious Diseases / Immunology / Pathology Disease Model Neuroscience / Behavior

2011 Experimental animals  
Therefore, both VHS and CTR are useful for evaluating the cardiac diseases in cynomolgus monkeys. 2P-43 Congenital Cardiac Diseases in Cynomolgus Monkey (Macaca fascicularis) Takashi Ikegawa 1 , Hiroshi  ...  prerequisites for researchers to facilitate rapid access to newly developed GER in Japan. 1P-30 Dispersion of the RIKEN-Modified SHIRPA for mouse comprehensive phenotyping Tomohiro -uzuki, -hizuka Nishimura, Yasuyo  ... 
doi:10.1538/expanim.60.275 fatcat:qhubhdt65rgefo6mnocs27neky