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

Research output: Contribution to journalArticle

7 Citations (Scopus)

Abstract

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. In addition to archiving the PDB data in collaboration with the other wwPDB partners, PDBj also provides a wide range of original and unique services and tools, which are continuously improved and updated. 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 surfaces, the extensions of the Omokage search for molecular shape similarity, and the integration of PDBj and BMRB searches.

Original languageEnglish
JournalProtein Science
DOIs
Publication statusAccepted/In press - 2017

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Japan
Databases
Proteins
User-Computer Interface
Static Electricity
Virtual reality
Electrostatics
Servers

Keywords

  • BMRB
  • PDB
  • Protein structures
  • Semantic web
  • Structural dynamics
  • Virtual reality

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

Cite this

Kinjo, A. R., Bekker, G. J., Wako, H., Endo, S., Tsuchiya, Y., Sato, H., ... Nakamura, H. (Accepted/In press). New tools and functions in data-out activities at Protein Data Bank Japan (PDBj). Protein Science. https://doi.org/10.1002/pro.3273

New tools and functions in data-out activities at Protein Data Bank Japan (PDBj). / Kinjo, Akira R.; Bekker, Gert Jan; Wako, Hiroshi; Endo, Shigeru; Tsuchiya, Yuko; Sato, Hiromu; Nishi, Hafumi; Kinoshita, Kengo; Suzuki, Hirofumi; Kawabata, Takeshi; Yokochi, Masashi; Iwata, Takeshi; Kobayashi, Naohiro; Fujiwara, Toshimichi; Kurisu, Genji; Nakamura, Haruki.

In: Protein Science, 2017.

Research output: Contribution to journalArticle

Kinjo, AR, Bekker, GJ, Wako, H, Endo, S, Tsuchiya, Y, Sato, H, Nishi, H, Kinoshita, K, Suzuki, H, Kawabata, T, Yokochi, M, Iwata, T, Kobayashi, N, Fujiwara, T, Kurisu, G & Nakamura, H 2017, 'New tools and functions in data-out activities at Protein Data Bank Japan (PDBj)', Protein Science. https://doi.org/10.1002/pro.3273
Kinjo, Akira R. ; Bekker, Gert Jan ; Wako, Hiroshi ; Endo, Shigeru ; Tsuchiya, Yuko ; Sato, Hiromu ; Nishi, Hafumi ; Kinoshita, Kengo ; Suzuki, Hirofumi ; Kawabata, Takeshi ; Yokochi, Masashi ; Iwata, Takeshi ; Kobayashi, Naohiro ; Fujiwara, Toshimichi ; Kurisu, Genji ; Nakamura, Haruki. / New tools and functions in data-out activities at Protein Data Bank Japan (PDBj). In: Protein Science. 2017.
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