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News on 2009-10-09

... ). This update is simultaneously made at every member of the wwPDB: RCSB-PDB, PDBe, and PDBj. On October 14, 2009, we will start to use ...

News on 2011-01-12

From January 15, 2011(JST), the wwPDB will resume the practice of providing advance notification of PDB entries that are about to be released in the following week.( wwPDB News... )

NMR Unified data

... a unified data file, the NMR data will be distributed in the PDB FTP area as single files in the NMR-STAR format. A best ...

News on 2005-12-28

RCSB-PDB mirror site in Osaka University, Japan is closed on Dec 28, 2005 (Japanese time). Please access PDBj site from now on.

[wwPDB] ModelCIF Extension for Computed Structure Models

... now available. The PDBx/mmCIF data standard underpins the Protein Data Bank (PDB) Core Archive, which is jointly managed by the worldwide Protein Data Bank ...

News on 2008-04-02

The articles of "Molecule of the Month: MOM", which are produced by Dr. David S. Goodsell and appear at the RCSB-PDB Web pages, are translated into Japanese by the PDBj staff and are open here.

Some hostnames have been deprecated

... sequence) promode.pdbj.org Promode Elastic (Database of normal mode analysis of PDB data)

News on 2011-04-13

Announcement: PDB Archive Version 4.0 to be Released Summer 2011 ( wwPDB News... )

News on 2006-02-27

Links to 3D-insight, GDB, KEGG are added to each result of the PDB browser (xPSSS).

Newsletter / Public Relations Resources

... 6 pages A4 12 pages) 2021 Calendar for celebrating 50th anniversary of PDB - - English A4 size, starts from Sunday (36MB) A4 size, starts from Monday ...

News on 2004-04-13

Functional Details Page is added in each result of the PDB browser (xPSSS).

News on 2011-06-17

Announcement: PDB Archive Version 4.0 to be Released July 13, 2011 ( wwPDB News... )

[wwPDB] Poster Prize Awarded at The Biophysical Society Meeting

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News on 2004-06-23

Functional Details Page has been revised for each result of the PDB browser(xPSSS), so that the correct chain names appear.

[wwPDB] Preprint Published on CryoEM Archiving and Validation Recommendations

... to provide overall quality percentile on map-model fitness compared to other PDB entries in the wwPDB validation report as the next step. [ wwPDB News ...

[wwPDB] Prizes Awarded at The Biophysical Society Japan Meeting

... , literary, charitable, and educational purposes. Consider supporting the next 50 years of PDB's spirit of openness, cooperation, and education with a donation to the ...

CIF tree tool

... can be seen with the PDBx/mmCIF files with PDBj's Mine PDB Explorer service. Besides PDBx/mmCIF other STAR formatted files should also work ...

PDBj Format conversion service now supports Chem Comp file.

PDBx/mmCIF Conversion service provided by PDBj now supports Chemical Component files in mmCIF format. The Chem Comp file in mmCIF format is converted to PDB format file.

[wwPDB] Deprecation of FTP File Download Protocol in the PDB Archive

The FTP protocol for file downloads has been losing popularity over the years in favor of HTTP/S. There are many advantages of HTTP/S including speed, statelessness, security (HTTPS), and better support. Importantly during the past 2-3 years the main web ...

[wwPDB] Deprecation of FTP File Download Protocol in the PDB Archive

The FTP protocol for file downloads has been losing popularity over the years in favor of HTTP/S. There are many advantages of HTTP/S including speed, statelessness, security (HTTPS), and better support. Importantly during the past 2-3 years the main web ...

The PDBj Mine2 relational database (RDB) now integrates the summary data of SIFTS developed by PDBe and UniProt.

... can easily retrieve, using SQL, various annotations of protein sequences in the PDB such as the Gene Ontology, taxonomy (biological species), structural classification (SCOP and ...

Mine 2 RDB local install

... (https://data.pdbj.org/pdbjplus/mine2/dump/). The following files are available: - PDB data: https://data.pdbj.org/pdbjplus/mine2/dump/pdbj.mine2.dump - chem ...

[wwPDB] Backbone Annotation and Standardization of Peptide Residues is Now Live

... have been updated accordingly. This improves the Findability and Interoperability of the PDB data and opens up new opportunities to use the updated peptide residue ...

[wwPDB] PDB50: Registration Open for Virtual Event

Throughout 2021, the wwPDB will be celebrating the 50th anniversary of the PDB archive. The inaugural symposium will be held May 4-5, 2021 in ...

The RDF version of SIFTS is now available at our FTP site ftp://ftp.pdbj.org/RDF/sifts/ .

... .org/RDF/sifts/. SIFTS provides various annotations of protein sequences in the PDB such as the Gene Ontology, taxonomy (biological species), structural classifications (SCOP and ...

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PDB entries from 2025-12-03

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