Protein Data Bank Japan: Improved tools for sequence‐oriented analysis of protein structures

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

Protein Science, 2025, 34(3), e70052

Number of Access:1,111（2025-08-16 03:18 Counts）

Identifier to cite or link to this item: https://hdl.handle.net/11094/100544

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Title
Protein Data Bank Japan: Improved tools for sequence‐oriented analysis of protein structures
Creator
NRID
1000080813758 1000080813758
ORCID
0000-0001-8385-5693 0000-0001-8385-5693
researchmap permalink
gjbekker gjbekker
Scopus Author ID
57190950837 57190950837
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
BMRB
EMDB
PDB
protein structure
sequence analyses
Description
Bekker Gert‐Jan, Nagao Chioko, Shirota Matsuyuki, et al. Protein Data Bank Japan: Improved tools for sequence‐oriented analysis of protein structures. Protein Science 34, e70052 (2025); https://doi.org/10.1002/pro.70052.
Abstract
Protein Data Bank Japan (PDBj) 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 recently introduced a new UniProt-integrated portal to provide users with a quick overview of their target protein and shows a recommended structure with integrated data from various internal and external resources. The portal page helps users identify known genomic variations of their protein of interest and provide insights into how these modifications might impact the structure, stability and dynamics of the protein. Furthermore, the portal page also helps users to select the optimal structure to use for further analysis. We have also introduced another service to explore proteins using experimental and computational approaches, which enables experimental structural biologists to increase their insight to help them to more efficiently design their experimental studies. With these new additions, we have enhanced our service portfolio to benefit both experimental and computational structural biologists in their search to interpret protein structures, their dynamics and function.
Publisher
Wiley
Source Title
Protein Science
Volume (Issue)
34(3)
Page
e70052
Date of Issued
2025-03-01
Language
English
Handle URL
https://hdl.handle.net/11094/100544
PISSN
09618368
eISSN
1469896X
Relation.isIdenticalTo
DOI (Publisher Version)
https://doi.org/10.1002/pro.70052
Access Rights
open access
CopyRight
This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
oaire:version
Version of Record
Category
学術雑誌論文 Journal Article