Protein Data Bank Japan (PDBj): Maintaining a Structural Data Archive and Resource Description Framework Format

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2011 Oct 7

PMID 21976737

Citations 71

Authors

Akira R Kinjo

Hirofumi Suzuki

Reiko Yamashita

Yasuyo Ikegawa

Takahiro Kudou

Reiko Igarashi

Yumiko Kengaku

Hasumi Cho

Daron M Standley

Atsushi Nakagawa

Haruki Nakamura

Affiliations

Soon will be listed here.

Abstract

The Protein Data Bank Japan (PDBj, http://pdbj.org) is a member of the worldwide Protein Data Bank (wwPDB) and accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins, which are summarized in this article. To enhance the interoperability of the PDB data, we have recently developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, along with its ontology in the Web Ontology Language (OWL) based on the PDB mmCIF Exchange Dictionary. Being in the standard format for the Semantic Web, the PDB/RDF data provide a means to integrate the PDB with other biological information resources.

Citing Articles

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

Bekker G, Nagao C, Shirota M, Nakamura T, Katayama T, Kihara D Protein Sci. 2025; 34(3):e70052.

PMID: 39969112 PMC: 11837027. DOI: 10.1002/pro.70052.

Identification and in vivo functional analysis of a novel missense mutation in GATA3 causing hypoparathyroidism, sensorineural deafness and renal dysplasia syndrome in a Chinese family.

Pan S, Long S, Cai L, Wen J, Lin W, Chen G Endocrine. 2024; 87(3):1194-1203.

PMID: 39505798 DOI: 10.1007/s12020-024-04087-6.

Quantum chemical calculation dataset for representative protein folds by the fragment molecular orbital method.

Takaya D, Ohno S, Miyagishi T, Tanaka S, Okuwaki K, Watanabe C Sci Data. 2024; 11(1):1164.

PMID: 39443514 PMC: 11499858. DOI: 10.1038/s41597-024-03999-2.

PDB NextGen Archive: centralizing access to integrated annotations and enriched structural information by the Worldwide Protein Data Bank.

Choudhary P, Feng Z, Berrisford J, Chao H, Ikegawa Y, Peisach E Database (Oxford). 2024; 2024.

PMID: 38803272 PMC: 11130521. DOI: 10.1093/database/baae041.

Prediction of Protein Function from Tertiary Structure of the Active Site in Heme Proteins by Convolutional Neural Network.

Kondo H, Iizuka H, Masumoto G, Kabaya Y, Kanematsu Y, Takano Y Biomolecules. 2023; 13(1).

PMID: 36671521 PMC: 9855806. DOI: 10.3390/biom13010137.

References

Velankar S, Alhroub Y, Alili A, Best C, Boutselakis H, Caboche S . PDBe: Protein Data Bank in Europe. Nucleic Acids Res. 2010; 39(Database issue):D402-10. PMC: 3013808. DOI: 10.1093/nar/gkq985. View

Kinoshita K, Nakamura H . eF-site and PDBjViewer: database and viewer for protein functional sites. Bioinformatics. 2004; 20(8):1329-30. DOI: 10.1093/bioinformatics/bth073. View

Lawson C, Baker M, Best C, Bi C, Dougherty M, Feng P . EMDataBank.org: unified data resource for CryoEM. Nucleic Acids Res. 2010; 39(Database issue):D456-64. PMC: 3013769. DOI: 10.1093/nar/gkq880. View

Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W . Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997; 25(17):3389-402. PMC: 146917. DOI: 10.1093/nar/25.17.3389. View

Katoh K, Toh H . Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform. 2008; 9(4):286-98. DOI: 10.1093/bib/bbn013. View

Katayama T, Wilkinson M, Vos R, Kawashima T, Kawashima S, Nakao M . The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications. J Biomed Semantics. 2011; 2:4. PMC: 3170566. DOI: 10.1186/2041-1480-2-4. View

Belleau F, Nolin M, Tourigny N, Rigault P, Morissette J . Bio2RDF: towards a mashup to build bioinformatics knowledge systems. J Biomed Inform. 2008; 41(5):706-16. DOI: 10.1016/j.jbi.2008.03.004. View

Good B, Wilkinson M . The Life Sciences Semantic Web is full of creeps!. Brief Bioinform. 2006; 7(3):275-86. DOI: 10.1093/bib/bbl025. View

Ito N, Phillips S, Stevens C, Ogel Z, McPherson M, Keen J . Novel thioether bond revealed by a 1.7 A crystal structure of galactose oxidase. Nature. 1991; 350(6313):87-90. DOI: 10.1038/350087a0. View

10.

Ulrich E, Akutsu H, Doreleijers J, Harano Y, Ioannidis Y, Lin J . BioMagResBank. Nucleic Acids Res. 2007; 36(Database issue):D402-8. PMC: 2238925. DOI: 10.1093/nar/gkm957. View

11.

Standley D, Kinjo A, Kinoshita K, Nakamura H . Protein structure databases with new web services for structural biology and biomedical research. Brief Bioinform. 2008; 9(4):276-85. DOI: 10.1093/bib/bbn015. View

12.

Katayama T, Arakawa K, Nakao M, Ono K, Aoki-Kinoshita K, Yamamoto Y . The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*. J Biomed Semantics. 2010; 1(1):8. PMC: 2939597. DOI: 10.1186/2041-1480-1-8. View

13.

Standley D, Yamashita R, Kinjo A, Toh H, Nakamura H . SeSAW: balancing sequence and structural information in protein functional mapping. Bioinformatics. 2010; 26(9):1258-9. PMC: 2859130. DOI: 10.1093/bioinformatics/btq116. View

14.

Kinoshita K, Murakami Y, Nakamura H . eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape. Nucleic Acids Res. 2007; 35(Web Server issue):W398-402. PMC: 1933152. DOI: 10.1093/nar/gkm351. View

15.

Rose P, Beran B, Bi C, Bluhm W, Dimitropoulos D, Goodsell D . The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res. 2010; 39(Database issue):D392-401. PMC: 3013649. DOI: 10.1093/nar/gkq1021. View

16.

Kinjo A, Yamashita R, Nakamura H . PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan. Database (Oxford). 2010; 2010:baq021. PMC: 2997606. DOI: 10.1093/database/baq021. View

17.

Wako H, Kato M, Endo S . ProMode: a database of normal mode analyses on protein molecules with a full-atom model. Bioinformatics. 2004; 20(13):2035-43. DOI: 10.1093/bioinformatics/bth197. View

18.

Kinjo A, Nakamura H . Geometric similarities of protein-protein interfaces at atomic resolution are only observed within homologous families: an exhaustive structural classification study. J Mol Biol. 2010; 399(3):526-40. DOI: 10.1016/j.jmb.2010.04.028. View

19.

Bairoch A, Apweiler R, Wu C, Barker W, Boeckmann B, Ferro S . The Universal Protein Resource (UniProt). Nucleic Acids Res. 2004; 33(Database issue):D154-9. PMC: 540024. DOI: 10.1093/nar/gki070. View

20.

Shannon P, Markiel A, Ozier O, Baliga N, Wang J, Ramage D . Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003; 13(11):2498-504. PMC: 403769. DOI: 10.1101/gr.1239303. View