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

15 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
Pages (from-to)95-102
Number of pages8
JournalProtein Science
Volume27
Issue number1
DOIs
Publication statusPublished - 2018 Jan

Keywords

  • BMRB
  • PDB
  • protein structures
  • semantic web
  • structural dynamics
  • virtual reality

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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    Kinjo, A. R., Bekker, G. J., 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. (2018). New tools and functions in data-out activities at Protein Data Bank Japan (PDBj). Protein Science, 27(1), 95-102. https://doi.org/10.1002/pro.3273