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7 results on '"Yasuyo Ikegawa"'

1. Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data

Author

Gert-Jan Bekker, Takahiro Kudou, Yasuyo Ikegawa, Takeshi Kawabata, Masashi Yokochi, Genji Kurisu, Hirofumi Suzuki, Kei Yura, Toshimichi Fujiwara, and Takeshi Iwata

Subjects
Models, Molecular, PDB, Open science, Protein Conformation, Computer science, Protein Data Bank (RCSB PDB), Biochemistry, World Wide Web, User-Computer Interface, Viral Proteins, Japan, COVID‐19, Pandemic, Animals, Humans, Databases, Protein, EMDB, Molecular Biology, Structure (mathematical logic), Tools for Protein Science, SARS-CoV-2, COVID-19, Proteins, computer.file_format, Protein Data Bank, Visualization, Outreach, Anniversaries and Special Events, BMRB, protein structures, User interface, computer, Software
Abstract

Protein Data Bank Japan (PDBj), a founding member of the worldwide Protein Data Bank (wwPDB) has accepted, processed and distributed experimentally determined biological macromolecular structures for 20 years. During that time, we have continuously made major improvements to our query search interface of PDBj Mine 2, the BMRBj web interface, and EM Navigator for PDB/BMRB/EMDB entries. PDBj also serves PDB‐related secondary database data, original web‐based modeling services such as Homology modeling of complex structure (HOMCOS), visualization services and utility tools, which we have continuously enhanced and expanded throughout the years. In addition, we have recently developed several unique archives, BSM‐Arc for computational structure models, and XRDa for raw X‐ray diffraction images, both of which promote open science in the structural biology community. During the COVID‐19 pandemic, PDBj has also started to provide feature pages for COVID‐19 related entries across all available archives at PDBj from raw experimental data and PDB structural data to computationally predicted models, while also providing COVID‐19 outreach content for high school students and teachers.

Published
2021
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2. Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB)

Author

Marcin Wojdyr, Paul D. Adams, David G. Brown, Zukang Feng, Yasuyo Ikegawa, Lora Mak, Minyu Chen, Billy K. Poon, John D. Westbrook, Ezra Peisach, Jasmine Young, Helen M. Berman, Masashi Yokochi, Nigel W. Moriarty, Yu-He Liang, Stephen K. Burley, John L. Markley, Garib N. Murshudov, John M. Berrisford, Eldon L. Ulrich, Sameer Velankar, Yumiko Kengaku, Aleksandras Gutmanas, Dorothee Liebschner, C. Flensburg, Pavel V. Afonine, Kumaran Baskaran, Clemens Vonrhein, Jeffrey C. Hoch, Eugene Krissinel, Irina Persikova, Genji Kurisu, Oleg V. Sobolev, Martin E.M. Noble, and Gérard Bricogne

Subjects
PDB, PDBx, Protein Conformation, Computer science, Biophysics, Protein Data Bank (RCSB PDB), Crystallography, X-Ray, 010402 general chemistry, 01 natural sciences, Databases, OneDep, 03 medical and health sciences, macromolecular crystallography, Protein Data Bank, Structural Biology, Humans, Letters to the Editor, Databases, Protein, Worldwide Protein Data Bank, 030304 developmental biology, PDBx/mmCIF format, validation, 0303 health sciences, Crystallography, Protein, biocuration, Macromolecular crystallography, Proteins, computer.file_format, mmCIF format, Biological Sciences, Data dictionary, 0104 chemical sciences, data archiving, Physical Sciences, Chemical Sciences, X-Ray, mmCIF, wwPDB, Database Management Systems, data dictionary, data standards, computer, Software
Abstract

This letter announces that PDBx/mmCIF format files will become mandatory for crystallographic depositions to the Protein Data Bank (PDB).

Published
2019
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3. Protein Data Bank: the single global archive for 3D macromolecular structure data

Author

Masashi Yokochi, Ju Yaen Kim, Chenghua Shao, John M. Berrisford, Hongyang Yao, Miron Livny, Stephen Anyango, Abhik Mukhopadhyay, Romana Gáborová, Yi-Ping Tao, Monica Sekharan, Aleksandras Gutmanas, Jose M. Dana, Mandar Deshpande, Charmi Bhikadiya, Yannis Ioannidis, Pedro Romero, Jonathan R. Wedell, Eldon L. Ulrich, Gert-Jan Bekker, Chris Randle, Chunxiao Bi, Jeffrey C. Hoch, Nurul Nadzirin, Jaroslav Koča, Yumiko Kengaku, Jasmine Young, Cole Christie, John D. Westbrook, Naohiro Kobayashi, Alexander S. Rose, Sameer Velankar, David Sehnal, Lukáš Pravda, David R. Armstrong, Hasumi Cho, Genji Kurisu, Lora Mak, John L. Markley, Saqib Mir, Sutapa Ghosh, Ardan Patwardhan, Zukang Feng, Stephen K. Burley, Robert Lowe, David S. Goodsell, Hirofumi Suzuki, Maria Voigt, Paul Gane, Jose M. Duarte, Osman Salih, Irina Periskova, Matthew J. Conroy, Toshimichi Fujiwara, Yasuyo Ikegawa, Takahiro Kudou, Dimitri Maziuk, Typhaine Paysan-Lafosse, Brian P. Hudson, Christine Zardecki, Sreenath Nair, Gerard J. Kleywegt, Marina A. Zhuravleva, Shuchismita Dutta, Dmytro Guzenko, Kumaran Baskaran, Rachel Kramer Green, Ezra Peisach, Li Chen, Reiko Yamashita, Vladimir Guranovic, Yu-He Liang, Takeshi Iwata, Atsushi Nakagawa, Haruki Nakamura, Junko Sato, Radka Svobodová Vařeková, Helen M. Berman, Deepti Gupta, Luigi Di Costanzo, Mihaly Varadi, Yana Valasatava, Burley, S. K., Berman, H. M., Bhikadiya, C., Bi, C., Chen, L., DI COSTANZO, Luigi, Addeo, PIETRO FRANCESCO BRUNO CHRISTI, Duarte, J. M., Dutta, S., Feng, Z., Ghosh, S., Goodsell, D. S., Green, R. K., Guranovic, V., Guzenko, D., Hudson, B. P., Liang, Y., Lowe, R., Peisach, E., Periskova, I., Randle, C., Rose, A., Sekharan, M., Shao, C., Tao, Y. -P., Valasatava, Y., Voigt, M., Westbrook, J., Young, J., Zardecki, C., Zhuravleva, M., Kurisu, G., Nakamura, H., Kengaku, Y., Cho, H., Sato, J., Kim, J. Y., Ikegawa, Y., Nakagawa, A., Yamashita, R., Kudou, T., Bekker, G. -J., Suzuki, H., Iwata, T., Yokochi, M., Kobayashi, N., Fujiwara, T., Velankar, S., Kleywegt, G. J., Anyango, S., Armstrong, D. R., Berrisford, J. M., Conroy, M. J., Dana, J. M., Deshpande, M., Gane, P., Gaborova, R., Gupta, D., Gutmanas, A., Koca, J., Mak, L., EL MIR, Abdelouahad, Mukhopadhyay, A., Nadzirin, N., Nair, S., Patwardhan, A., Paysan-Lafosse, T., Pravda, L., Salih, O., Sehnal, D., Varadi, M., Varekova, R., Markley, J. L., Hoch, J. C., Romero, P. R., Baskaran, K., Maziuk, D., Ulrich, E. L., Wedell, J. R., Sicong, Yao, Livny, M., and Ioannidis, Y. E.

Subjects
Models, Molecular, Protein Conformation, Molecular Conformation, Protein Data Bank (RCSB PDB), Master data, Biology, computer.software_genre, 03 medical and health sciences, 0302 clinical medicine, Genetics, Database Issue, RDF, Databases, Protein, 030304 developmental biology, Structure (mathematical logic), 0303 health sciences, Database, Experimental data, DNA, computer.file_format, Atomic coordinates, Protein Data Bank, Metadata, Metals, Nucleic Acid Conformation, RNA, computer, 030217 neurology & neurosurgery
Abstract

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; wwpdb.org), 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 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.

Published
2018
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4. Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures

Author

Gert-Jan Bekker, Haruki Nakamura, Hirofumi Suzuki, Takeshi Kawabata, Yasuyo Ikegawa, Yuko Tsuchiya, and Akira R. Kinjo

Subjects
Models, Molecular, 0301 basic medicine, Protein Conformation, Relational database, Interoperability, Protein Data Bank (RCSB PDB), Web Browser, Biology, computer.software_genre, Structure-Activity Relationship, User-Computer Interface, 03 medical and health sciences, Software, Japan, Genetics, Database Issue, RDF, Databases, Protein, Database, business.industry, computer.file_format, Protein Data Bank, 030104 developmental biology, Web service, User interface, business, computer
Abstract

The Protein Data Bank Japan (PDBj, http://pdbj.org), a member of the worldwide Protein Data Bank (wwPDB), 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 database 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.

Published
2016
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5. OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive

Author

Marina Zhuravleva, Ezra Peisach, Monica Sekharan, Glen van Ginkel, Reiko Igarashi, Jasmine Young, M. Saqib Mir, Lora Mak, Dimitris Dimitropoulos, Raul Sala, David R. Armstrong, Sanchayita Sen, Sameer Velankar, Gerard J. Kleywegt, Li Chen, Lihua Tan, Swanand Gore, Reiko Yamashita, Sutapa Ghosh, Eduardo Sanz-García, Zukang Feng, John D. Westbrook, Vladimir Guranovic, Yu-He Liang, Aleksandras Gutmanas, Thomas J. Oldfield, Brian P. Hudson, Huanwang Yang, Minyu Chen, Guanghua Gao, G. Jawahar Swaminathan, Eldon L. Ulrich, Yasuyo Ikegawa, Naohiro Kobayashi, Irina Persikova, Luigi Di Costanzo, Steve Mading, John L. Markley, Chenghua Shao, Helen M. Berman, Luana Rinaldi, Ardan Patwardhan, John M. Berrisford, Abhik Mukhopadhyay, Haruki Nakamura, Stephen K. Burley, Catherine L. Lawson, Pieter M. S. Hendrickx, Martha Quesada, Young, J. Y., Westbrook, J. D., Feng, Z., Sala, R., Peisach, E., Oldfield, T. J., Sen, S., Gutmanas, A., Armstrong, D. R., Berrisford, J. M., Chen, L., Chen, M., DI COSTANZO, Luigi, Dimitropoulos, D., Gao, G., Ghosh, S., Gore, S., Guranovic, V., Hendrickx, P. M. S., Hudson, B. P., Igarashi, R., Ikegawa, Y., Kobayashi, N., Lawson, C. L., Liang, Y., Mading, S., Mak, L., Mir, M. S., Mukhopadhyay, A., Patwardhan, A., Persikova, I., Rinaldi, L., Sanz-Garcia, E., Sekharan, M. R., Shao, C., Swaminathan, G. J., Tan, L., Ulrich, E. L., van Ginkel, G., Yamashita, R., Yang, H., Zhuravleva, M. A., Quesada, M., Kleywegt, G. J., Berman, H. M., Markley, J. L., Nakamura, H., Velankar, S., and Burley, S. K.

Subjects
0301 basic medicine, Models, Molecular, data deposition, PDB, Computer science, Protein Conformation, Protein Data Bank (RCSB PDB), Article, 03 medical and health sciences, User-Computer Interface, Average size, Protein Data Bank, structural biology, Databases, Protein, Molecular Biology, Nuclear Magnetic Resonance, Biomolecular, Data Curation, Research data, validation, Internet, business.industry, biocuration, Protein, Proteins, computer.file_format, research data, 3D macromolecular structure, Unified system, data archiving, 030104 developmental biology, wwPDB, Software engineering, business, computer
Abstract

OneDep, a unified system for deposition, biocuration, and validation of experimentally determined structures of biological macromolecules to the Protein Data Bank (PDB) archive, has been developed as a global collaboration by the Worldwide Protein Data Bank (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 deposition 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.

Published
2018
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6. Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data

Author

Marina Zhuravleva, Raul Sala, Lora Mak, Stephen K. Burley, Monica Sekharan, Oliver S. Smart, Brian P. Hudson, Ardan Patwardhan, Gerard J. Kleywegt, Alice R. Clark, Guanghua Gao, Kumaran Baskaran, Sutapa Ghosh, David R. Armstrong, Kayoko Nishiyama, John M. Berrisford, Ezra Peisach, Abhik Mukhopadhyay, G. Jawahar Swaminathan, Huanwang Yang, Minyu Chen, Catherine L. Lawson, Thomas J. Oldfield, Junko Sato, Zukang Feng, Helen M. Berman, Yumiko Kengaku, Chenghua Shao, Glen van Ginkel, Irina Persikova, John L. Markley, Genji Kurisu, Yasuyo Ikegawa, Jasmine Young, Pieter M. S. Hendrickx, Luigi Di Costanzo, Aleksandras Gutmanas, John D. Westbrook, Reiko Igarashi, Buvaneswari Coimbatore Narayanan, Li Chen, Eduardo Sanz-García, Vladimir Guranovic, Yu-He Liang, Haruki Nakamura, Gaurav Sahni, Sameer Velankar, Sanchayita Sen, Lihua Tan, Swanand Gore, Dimitris Dimitropoulos, Young, J. Y., Westbrook, J. D., Feng, Z., Peisach, E., Persikova, I., Sala, R., Sen, S., Berrisford, J. M., Swaminathan, G. J., Oldfield, T. J., Gutmanas, A., Igarashi, R., Armstrong, D. R., Baskaran, K., Chen, L., Chen, M., Clark, A. R., DI COSTANZO, Luigi, Dimitropoulos, D., Gao, G., Ghosh, S., Gore, S., Guranovic, V., Hendrickx, P. M. S., Hudson, B. P., Ikegawa, Y., Kengaku, Y., Lawson, C. L., Liang, Y., Mak, L., Mukhopadhyay, A., Narayanan, B., Nishiyama, K., Patwardhan, A., Sahni, G., Sanz-Garcia, E., Sato, J., Sekharan, M. R., Shao, C., Smart, O. S., Tan, L., Van Ginkel, G., Yang, H., Zhuravleva, M. A., Markley, J. L., Nakamura, H., Kurisu, G., Kleywegt, G. J., Velankar, S., Berman, H. M., and Burley, S. K.

Subjects
0301 basic medicine, Vocabulary, Data curation, Protein Conformation, Extramural, Computer science, media_common.quotation_subject, MEDLINE, computer.file_format, Protein Data Bank, Data science, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, 030104 developmental biology, Vocabulary, Controlled, Structural biology, Original Article, Quality (business), Databases, Protein, General Agricultural and Biological Sciences, computer, Data Curation, Information Systems, media_common
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 worldwide PDB (wwPDB) is the international collaboration that manages the PDB archive according to the FAIR principles: Findability, Accessibility, 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 high-quality 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: https://www.wwpdb.org/

Published
2018
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7. Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format

Author

Daron M. Standley, Yumiko Kengaku, Takahiro Kudou, Yasuyo Ikegawa, Reiko Yamashita, Atsushi Nakagawa, Haruki Nakamura, Akira R. Kinjo, Hirofumi Suzuki, Reiko Igarashi, and Hasumi Cho

Subjects
Internet, business.industry, Protein Conformation, Interoperability, Protein Data Bank (RCSB PDB), Proteins, computer.file_format, Articles, Ontology language, Biology, Ontology (information science), Protein Data Bank, World Wide Web, User-Computer Interface, Genetics, The Internet, RDF, business, Databases, Protein, computer, Semantic Web, Software
Abstract

The Protein Data Bank Japan (PDBj, http://pdbj.org) is a member of the worldwide Protein Data Bank (wwPDB) and 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, which are summarized in this article. To enhance the interoperability of the PDB data, we have recently developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, along with its ontology in the Web Ontology Language (OWL) based on the PDB mmCIF Exchange Dictionary. Being in the standard format for the Semantic Web, the PDB/RDF data provide a means to integrate the PDB with other biological information resources.

Published
2011

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