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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, http://pdbj.org), 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.  ...  ACKNOWLEDGEMENTS The authors thank the PDBj annotators, Reiko Igarashi, Yumiko Kengaku, Hasumi Cho, Junko Sato for their constant effort that makes the wwPDB possible at all, and Reiko Yamashita and Takahiro  ... 
doi:10.1093/nar/gkw962 pmid:27789697 pmcid:PMC5210648 fatcat:pan6qdrpe5bknfgkot6blgnp6u

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

A. R. Kinjo, H. Suzuki, R. Yamashita, Y. Ikegawa, T. Kudou, R. Igarashi, Y. Kengaku, H. Cho, D. M. Standley, A. Nakagawa, H. Nakamura
2011 Nucleic Acids Research  
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  ...  FUNDING Funding for open access charge: National Bioscience Database Center, the Japan Science and Technology Agency. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkr811 pmid:21976737 pmcid:PMC3245181 fatcat:rgdsfxvkfvhgnnpag3funh52pu

New tools and functions in data-out activities at Protein Data Bank Japan (PDBj)

Akira R. Kinjo, Gert-Jan Bekker, Hiroshi Wako, Shigeru Endo, Yuko Tsuchiya, Hiromu Sato, Hafumi Nishi, Kengo Kinoshita, Hirofumi Suzuki, Takeshi Kawabata, Masashi Yokochi, Takeshi Iwata (+4 others)
2017 Protein Science  
The Protein Data Bank Japan (PDBj), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined biological macromolecular structures.  ...  Here, we report the new RDB PDBj Mine 2, the WebGL molecular viewer Molmil, the ProMode-Elastic server for normal mode analysis, a virtual reality system for the eF-site protein electrostatic molecular  ...  Introduction The Protein Data Bank Japan (PDBj, https://pdbj. org/) 1,2 accepts and annotates biological macromolecular structure data in collaboration with the other worldwide Protein Data Bank (wwPDB  ... 
doi:10.1002/pro.3273 pmid:28815765 pmcid:PMC5734392 fatcat:7ttn55ucxvcjfjkmivznvmet34

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows

Toshiaki Katayama, Kazuharu Arakawa, Mitsuteru Nakao, Keiichiro Ono, Kiyoko F Aoki-Kinoshita, Yasunori Yamamoto, Atsuko Yamaguchi, Shuichi Kawashima, Hong-Woo Chun, Jan Aerts, Bruno Aranda, Load Hendrix Barboza (+45 others)
2010 Journal of Biomedical Semantics  
systems without the need to transfer entire databases for every step of an analysis.  ...  However, various incompatibilities among database resources and analysis services make it difficult to connect and integrate these into interoperable workflows.  ...  Center (CBRC), National Institute of Advanced Industrial Science and Technology, Japan.  ... 
doi:10.1186/2041-1480-1-8 pmid:20727200 pmcid:PMC2939597 fatcat:ytcct7auwbexdf4qwcvhl4ac4a

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  ...  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  ...  ACKNOWLEDGEMENTS The authors thank all the members of Worldwide PDB for their support and feedback, especially Kumaran Baskaran, Toshimichi Fujiwara, Takeshi  ... 
doi:10.1016/j.str.2017.01.004 pmid:28190782 pmcid:PMC5360273 fatcat:okamctypwvdrxfomgjio4rsvma

The RCSB Protein Data Bank: redesigned web site and web services

P. W. Rose, B. Beran, C. Bi, W. F. Bluhm, D. Dimitropoulos, D. S. Goodsell, A. Prlic, M. Quesada, G. B. Quinn, J. D. Westbrook, J. Young, B. Yukich (+3 others)
2010 Nucleic Acids Research  
The RCSB Protein Data Bank (RCSB PDB) web site (http://www.pdb.org) has been redesigned to increase usability and to cater to a larger and more diverse user base.  ...  This article describes key enhancements and new features that fall into the following categories: (i) query and analysis tools for chemical structure searching, query refinement, tabulation and export  ...  ACKNOWLEDGEMENTS We are grateful to ChemAxon (http://www.chemaxon .com) for providing Marvin Sketch, JChem Base and Standardizer for the chemical-structure search.  ... 
doi:10.1093/nar/gkq1021 pmid:21036868 pmcid:PMC3013649 fatcat:aciwaivaenfubmhs2r3tc37qiu

PDBe: Protein Data Bank in Europe

S. Velankar, C. Best, B. Beuth, C. H. Boutselakis, N. Cobley, A. W. Sousa Da Silva, D. Dimitropoulos, A. Golovin, M. Hirshberg, M. John, E. B. Krissinel, R. Newman (+13 others)
2009 Nucleic Acids Research  
of bio-macromolecular structure data, the Protein Data Bank (PDB).  ...  PDBe's active involvement with the X-ray crystallography, Nuclear Magnetic Resonance spectroscopy and cryo-Electron Microscopy communities have resulted in improved tools for structure deposition and analysis  ...  (BMRB) (3) in the USA, and the Protein Data Bank Japan (PDBj), collectively form the Worldwide Protein Data Bank (wwPDB) (4) organization. wwPDB is responsible for maintaining the single worldwide repository  ... 
doi:10.1093/nar/gkp916 pmid:19858099 pmcid:PMC2808887 fatcat:amgz3equ6jgenhym77vbghy47e

Toolboxes for a standardised and systematic study of glycans

Matthew P Campbell, René Ranzinger, Thomas Lütteke, Julien Mariethoz, Catherine A Hayes, Jingyu Zhang, Yukie Akune, Kiyoko F Aoki-Kinoshita, David Damerell, Giorgio Carta, Will S York, Stuart M Haslam (+5 others)
2014 BMC Bioinformatics  
Automation of structure analysis then calls for software development since adding meaning to large data collections in reasonable time requires corresponding bioinformatics methods and tools.  ...  Current glycobioinformatics resources do cover information on the structure and function of glycans, their interaction with proteins or their enzymatic synthesis.  ...  UniCarbKB is supported by the Australian National eResearch Collaboration Tools and Resources project (NeCTAR).  ... 
doi:10.1186/1471-2105-15-s1-s9 pmid:24564482 pmcid:PMC4016020 fatcat:yklyisg7lfdxrb4cpgldufvrve

Semantic Web technologies for the big data in life sciences

Hongyan Wu, Atsuko Yamaguchi
2014 BioScience Trends  
large-scale data.  ...  To ensure that big data has a major influence in the life sciences, comprehensive data analysis across multiple data sources and even across disciplines is indispensable.  ...  Acknowledgements This work has been supported by the National Bioscience Database Center (NBDC) of the Japan Science and Technology Agency (JST).  ... 
doi:10.5582/bst.2014.01048 fatcat:x2rlpyjel5cybarma34ji6sq3y

Implementation of linked data in the life sciences at BioHackathon 2011

Kiyoko F Aoki-Kinoshita, Akira R Kinjo, Mizuki Morita, Yoshinobu Igarashi, Yi-an Chen, Yasumasa Shigemoto, Takatomo Fujisawa, Yukie Akune, Takeo Katoda, Anna Kokubu, Takaaki Mori, Mitsuteru Nakao (+4 others)
2015 Journal of Biomedical Semantics  
As a part of the Semantic Web, data are linked so that a person or machine can explore the web of data. Resource Description Framework (RDF) is the standard means of implementing Linked Data.  ...  For the database provider, such interoperability will surely lead to an increase in the number of users.  ...  * PDBj The Protein Data Bank Japan (PDBj), a member of the worldwide Protein Data Bank (wwPDB), is a database of atomic structures of proteins and other biological macromolecules.  ... 
doi:10.1186/2041-1480-6-3 pmid:25973165 pmcid:PMC4429360 fatcat:hrwxw6k25jfmpkbsdr22yn4a7y

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  
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.  ...  Acknowledgements The authors thank all the members of the worldwide Protein Data Bank (wwPDB) for their support and feedback, Kim Henrick for his direction to the PDB in Europe (PDBe) biocuration team  ... 
doi:10.1093/database/bay002 pmid:29688351 pmcid:PMC5804564 fatcat:pymncvy65zghjgdhleavnz7oce

Three-Dimensional Structures of Carbohydrates and Where to Find Them

Sofya I. Scherbinina, Philip V. Toukach
2020 International Journal of Molecular Sciences  
Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology.  ...  Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.  ...  Tool Description Type a Reference Structural data analysis Conformational Analysis Tool (CAT) Analysis of carbohydrate molecular trajectory data derived from MD simulations Standalone software [279] (http  ... 
doi:10.3390/ijms21207702 pmid:33081008 fatcat:sympabhcbzd47k4ll4h2gqiwkq

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies

Toshiaki Katayama, Mark D Wilkinson, Gos Micklem, Shuichi Kawashima, Atsuko Yamaguchi, Mitsuteru Nakao, Yasunori Yamamoto, Shinobu Okamoto, Kenta Oouchida, Hong-Woo Chun, Jan Aerts, Hammad Afzal (+54 others)
2013 Journal of Biomedical Semantics  
We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization.  ...  those data using their tools and interfaces.  ...  RDF The Resource Description Framework (RDF) is a data model proposed by the W3C to implement and support the Semantic Web infrastructure.  ... 
doi:10.1186/2041-1480-4-6 pmid:23398680 pmcid:PMC3598643 fatcat:fm5xaotu3nbafibe3pm3js4d7u

Evolution of web services in bioinformatics

P. B. T. Neerincx
2005 Briefings in Bioinformatics  
Owing to the lack of standards for data sets and the interfaces of the tools this is not a trivial task.  ...  Bioinformaticians have developed large collections of tools to make sense of the rapidly growing pool of molecular biological data.  ...  in the Protein Data Bank (PDB). 26 One of the members of the PDB organisation, Protein Data Bank Japan (PDBj), has developed a tool called xPSSSS that provides a SOAPbased service to retrieve PDBML  ... 
doi:10.1093/bib/6.2.178 pmid:15975226 fatcat:alotxt4xurbbxavufbwrm6k6my

RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences

Stephen K Burley, Charmi Bhikadiya, Chunxiao Bi, Sebastian Bittrich, Li Chen, Gregg V Crichlow, Cole H Christie, Kenneth Dalenberg, Luigi Di Costanzo, Jose M Duarte, Shuchismita Dutta, Zukang Feng (+26 others)
2020 Nucleic Acids Research  
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), the US data center for the global PDB archive and a founding member of the Worldwide Protein Data Bank partnership  ...  New features and resources are described in detail using examples that showcase recently released structures of SARS-CoV-2 proteins and host cell proteins relevant to understanding and addressing the COVID  ...  Protein Data Bank partners.  ... 
doi:10.1093/nar/gkaa1038 pmid:33211854 pmcid:PMC7779003 fatcat:dkqo54quqjgovp7y4v67b635zu
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