Protein Data Bank Japan : Computational Resources for Analysis of Protein Structures

Bekker, Gert Jan; Nagao, Chioko; Shirota, Matsuyuki et al.

Journal of Molecular Biology, 2025, 169013

Number of Access:863（2025-08-16 03:17 Counts）

Identifier to cite or link to this item: https://hdl.handle.net/11094/100980

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Title
Protein Data Bank Japan : Computational Resources for Analysis of Protein Structures
Creator
CreatorName
Bekker, Gert Jan
NRID
1000010402463 1000010402463
ORCID
0000-0002-7721-0642 0000-0002-7721-0642
researchmap permalink
c_nagao c_nagao
Scopus Author ID
14520710200 14520710200
CreatorName
Nagao, Chioko
NRID
1000000549462 1000000549462
CreatorName
Shirota, Matsuyuki
NRID
1000040852471 1000040852471
CreatorName
Nakamura, Tsukasa
NRID
1000060396869 1000060396869
CreatorName
Katayama, Toshiaki
ORCID
0000-0003-4091-6614 0000-0003-4091-6614
CreatorName
Kihara, Daisuke
NRID
1000060332293 1000060332293
CreatorName
Kinoshita, Kengo
NRID
1000090294131 1000090294131
ORCID
0000-0002-5354-0807 0000-0002-5354-0807
researchmap permalink
read0051718 read0051718
Scopus Author ID
6701675123 6701675123
CreatorName
Kurisu, Genji
Subject
data archives
PDB
protein structure
sequence analyses
UniProt
Description
Bekker G.J., Nagao C., Shirota M., et al. Protein Data Bank Japan: Computational Resources for Analysis of Protein Structures. Journal of Molecular Biology , 169013 (2025); https://doi.org/10.1016/j.jmb.2025.169013.
Abstract
Protein Data Bank Japan (PDBj, https://pdbj.org/) is the Asian hub of three-dimensional macromolecular structure data, and a founding member of the worldwide Protein Data Bank. We have accepted, processed, and distributed experimentally determined biological macromolecular structures for over two decades. Although we collaborate with RCSB PDB and BMRB in the United States, PDBe and EMDB in Europe and recently PDBc in China for our data-in activities, we have developed our own unique services and tools for searching, exploring, visualizing, and analyzing protein structures. We have also developed novel archives for computational data and raw crystal diffraction images. Recently, we introduced the Sequence Navigator Pro service to explore proteins using experimental and computational approaches, which enables experimental structural biologists to increase their insight to help them to design their experimental studies more efficiently. In addition, we also introduced a new UniProt-integrated portal to provide users with a quick overview of their target protein and it shows a recommended structure and integrates data from various internal and external resources. With these new additions, we have enhanced our service portfolio to benefit both experimental as computational structural biologists in their search to interpret protein structures, their dynamics and function.
Publisher
Academic Press
Source Title
Journal of Molecular Biology
Page
169013
Date of Issued
2025-02-15
Language
English
Handle URL
https://hdl.handle.net/11094/100980
PISSN
00222836
eISSN
10898638
Relation.isIdenticalTo
DOI (Publisher Version)
https://doi.org/10.1016/j.jmb.2025.169013
Access Rights
open access
CopyRight
This article is licensed under a Creative Commons Attribution 4.0 International License.
oaire:version
Version of Record
Category
学術雑誌論文 Journal Article