H
Hirofumi Suzuki
Researcher at Osaka University
Publications - 6
Citations - 889
Hirofumi Suzuki is an academic researcher from Osaka University. The author has contributed to research in topics: Protein Data Bank & Protein Data Bank (RCSB PDB). The author has an hindex of 5, co-authored 5 publications receiving 559 citations.
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Journal ArticleDOI
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,Rachel Kramer Green,Vladimir Guranovic,Dmytro Guzenko,Brian P. Hudson,Yu-He Liang,Robert Lowe,Ezra Peisach,Irina Periskova,Chris Randle,Alexander S. Rose,Monica Sekharan,Chenghua Shao,Yi-Ping Tao,Yana Valasatava,Maria Voigt,John D. Westbrook,Jasmine Young,Christine Zardecki,Marina A. Zhuravleva,Genji Kurisu,Haruki Nakamura,Yumiko Kengaku,Hasumi Cho,Junko Sato,Ju Yaen Kim,Yasuyo Ikegawa,Atsushi Nakagawa,Reiko Yamashita,Takahiro Kudou,Gert-Jan Bekker,Hirofumi Suzuki,Takeshi Iwata,Masashi Yokochi,Naohiro Kobayashi,Toshimichi Fujiwara,Sameer Velankar,Gerard J. Kleywegt,Stephen Anyango,David R. Armstrong,John M. Berrisford,Matthew J. Conroy,Jose M. Dana,Mandar Deshpande,Paul Gane,Romana Gáborová,Deepti Gupta,Aleksandras Gutmanas,Jaroslav Koča,Lora Mak,Saqib Mir,Abhik Mukhopadhyay,Nurul Nadzirin,Sreenath Nair,Ardan Patwardhan,Typhaine Paysan-Lafosse,Lukáš Pravda,Osman Salih,David Sehnal,Mihaly Varadi,Radka Svobodová Vařeková,John L. Markley,Jeffrey C. Hoch,Pedro Romero,Kumaran Baskaran,Dimitri Maziuk,Eldon L. Ulrich,Jonathan R. Wedell,Hongyang Yao,Miron Livny,Yannis Ioannidis +81 more
TL;DR: Impacts of the recently developed universal wwPDB OneDep deposition/validation/biocuration system and various methods-specific ww PDB 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.
Journal ArticleDOI
Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format
Akira R. Kinjo,Hirofumi Suzuki,Reiko Yamashita,Yasuyo Ikegawa,Takahiro Kudou,Reiko Igarashi,Yumiko Kengaku,Hasumi Cho,Daron M. Standley,Atsushi Nakagawa,Haruki Nakamura +10 more
TL;DR: The Protein Data Bank Japan has 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.
Journal ArticleDOI
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 +6 more
TL;DR: The updated web user interfaces together with RESTful web services and the backend relational database that support the former are outlined and enhanced the connectivity of the wwPDB/RDF data by incorporating various external data resources.
Journal ArticleDOI
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,Naohiro Kobayashi,Toshimichi Fujiwara,Genji Kurisu,Haruki Nakamura +15 more
TL;DR: 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 surfaces, the extensions of the Omokage search for molecular shape similarity, and the integration of PDBJ and BMRB searches are reported.
Journal ArticleDOI
Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB
TL;DR: Omokage search is a service to search the global shape similarity of biological macromolecules and their assemblies, in both the Protein Data Bank and Electron Microscopy Data Bank, which provides new structural perspectives to life science researchers.