N
Naohiro Kobayashi
Researcher at Osaka University
Publications - 51
Citations - 2226
Naohiro Kobayashi is an academic researcher from Osaka University. The author has contributed to research in topics: RNA & Protein structure. The author has an hindex of 21, co-authored 51 publications receiving 1654 citations. Previous affiliations of Naohiro Kobayashi include Yokohama City University & Frankfurt Institute for Advanced Studies.
Papers
More filters
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
Validation of Structures in the Protein Data Bank
Swanand Gore,Eduardo Sanz Garcia,Pieter M. S. Hendrickx,Aleksandras Gutmanas,John D. Westbrook,Huanwang Yang,Zukang Feng,Kumaran Baskaran,John M. Berrisford,Brian P. Hudson,Yasuyo Ikegawa,Naohiro Kobayashi,Catherine L. Lawson,Steve Mading,Lora Mak,Abhik Mukhopadhyay,Thomas J. Oldfield,Ardan Patwardhan,Ezra Peisach,Gaurav Sahni,Monica Sekharan,Sanchayita Sen,Chenghua Shao,Oliver S. Smart,Eldon L. Ulrich,Reiko Yamashita,Martha Quesada,Jasmine Young,Haruki Nakamura,John L. Markley,Helen M. Berman,Stephen K. Burley,Sameer Velankar,Gerard J. Kleywegt +33 more
TL;DR: The Worldwide PDB recently launched a deposition, biocuration, and validation tool: OneDep, which provides useful metrics with which depositors can evaluate the quality of the experimental data, the structural model, and the fit between them.
Journal ArticleDOI
KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies.
Naohiro Kobayashi,Junji Iwahara,Junji Iwahara,Seizo Koshiba,Tadashi Tomizawa,Naoya Tochio,Peter Güntert,Takanori Kigawa,Shigeyuki Yokoyama +8 more
TL;DR: The new software KUJIRA, a package of integrated modules for the systematic and interactive analysis of NMR data, is developed, designed to reduce the tediousness of organizing and manipulating a large number of N MR data sets, which led to increased reliability of the determined structure.
Journal ArticleDOI
Structural insight into the zinc finger CW domain as a histone modification reader.
Fahu He,Takashi Umehara,Kohei Saito,Takushi Harada,Satoru Watanabe,Takashi Yabuki,Takanori Kigawa,M. Takahashi,Kanako Kuwasako,Kengo Tsuda,Takayoshi Matsuda,Masaaki Aoki,Eiko Seki,Naohiro Kobayashi,Peter Güntert,Shigeyuki Yokoyama,Yutaka Muto +16 more
TL;DR: The zinc finger CW (zf-CW) domain is a motif of about 60 residues that is frequently found in proteins involved in epigenetic regulation and is identified as a member of the histone modification reader modules for epigeneticregulation.
Journal ArticleDOI
OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive
Jasmine 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,Luigi Di Costanzo,Dimitris Dimitropoulos,Guanghua Gao,Sutapa Ghosh,Swanand Gore,Vladimir Guranovic,Pieter M. S. Hendrickx,Brian P. Hudson,Reiko Igarashi,Yasuyo Ikegawa,Naohiro Kobayashi,Catherine L. Lawson,Yu-He Liang,Steve Mading,Lora Mak,M. Saqib Mir,Abhik Mukhopadhyay,Ardan Patwardhan,Irina Persikova,Luana Rinaldi,Eduardo Sanz-García,Monica Sekharan,Chenghua Shao,G. Jawahar Swaminathan,Lihua Tan,Eldon L. Ulrich,Glen van Ginkel,Reiko Yamashita,Huanwang Yang,Marina Zhuravleva,Martha Quesada,Gerard J. Kleywegt,Helen M. Berman,John L. Markley,Haruki Nakamura,Sameer Velankar,Stephen K. Burley +48 more
TL;DR: The design, functional operation, and supporting infrastructure of the OneDep system are described, and initial performance assessments are provided.