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PDBj specifications


Unique identifier OMICS_07430
Name PDBj
Alternative name Protein Data Bank Japan
Restrictions to use None
Maintained Yes


  • person_outline Haruki kamura

Publications for Protein Data Bank Japan

PDBj citations


Caveat Usor: Assessing Differences between Major Chemistry Databases

PMCID: 5900829
PMID: 29451740
DOI: 10.1002/cmdc.201700724

[…] mit all the heteroatom structures (HETATM). These encompass resolved small molecules including salts and reagents. Secondly, there are four different sources within wwPDB and the NCBI. While PDBe and PDBj counts are more or less concordant at 25 057 and 25 252, respectively, RCSB PDB drops slightly to 24 140. It is not clear which of these sets was loaded into CS on the 25th of May, but UC refresh […]


Positive Charges on the Surface of Thaumatin Are Crucial for the Multi Point Interaction with the Sweet Receptor

Front Mol Biosci
PMCID: 5816810
PMID: 29487853
DOI: 10.3389/fmolb.2018.00010
call_split See protocol

[…] L (DeLano, ). The analysis of Poisson-Boltzmann electrostatics calculations was performed using PDB2PQR Server (Dolinsky et al., ). The coordinates and observed intensities have been deposited in the PDBj (PDB ID, 5YYQ for K78A, and 5YYR for K106A, and 5YYP for K137A). […]


PDBe: towards reusable data delivery infrastructure at protein data bank in Europe

Nucleic Acids Res
PMCID: 5753225
PMID: 29126160
DOI: 10.1093/nar/gkx1070

[…] ctions will display the exact number of atomic contacts in that particular interaction.Links to wwPDB partners: A simple component which shows links to the three wwPDB sites providing PDB data: PDBe, PDBj and RCSB PDB.PDB_REDO: The PDB_REDO component shows the change in geometric quality and in fit to experimental data between the original PDB entry and the automatically re-refined model available […]


New tools and functions in data‐out activities at Protein Data Bank Japan (PDBj)

PMCID: 5734392
PMID: 28815765
DOI: 10.1002/pro.3273

[…] First, we describe our updated system of the relational database (RDB), PDBj Mine 2 that processes many different kind of queries about the PDB metadata. In order to integrate the PDB data with other biological information, it includes the resource of SIFTS (Structure int […]


Neuro symbolic representation learning on biological knowledge graphs

PMCID: 5860058
PMID: 28449114
DOI: 10.1093/bioinformatics/btx275

[…] . were supported by funding from King Abdullah University of Science and Technology (KAUST). A.R.K. was supported by Database Integration Coordination Program (Upgrading and Integrative Management of Protein Data Bank Japan) from the National Bioscience Database Center (NBDC) and Platform Project for Supporting in Drug Discovery and Life Science Research (Platform for Drug Discovery, Informatics, […]


Modern Technologies of Solution Nuclear Magnetic Resonance Spectroscopy for Three dimensional Structure Determination of Proteins Open Avenues for Life Scientists

Comput Struct Biotechnol J
PMCID: 5408130
PMID: 28487762
DOI: 10.1016/j.csbj.2017.04.001

[…] ifornia, San Francisco), CARA (developed by Dr. Keller of the Kurt Wüthrich's group, http://cara.nmr-software.org/portal/), NMRView , and Kujira and MagRO (developed by Prof. Naohiro Kobayashi of the PDBj-BMRB group (Osaka University, Japan), http://bmrbdep.pdbj.org/en/nmr_tool_box/magro_nmrview.html) , with NMRView and CcpNmr (http://www.ccpn.ac.uk/). Programs for automated assignment of backbon […]


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PDBj institution(s)
Institute for Protein Research and Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan

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