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[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 ...

PDBx/mmCIF Resources

The wwPDB is going to start to use a new standard format, PDBx/mmCIF in 2014, replacing the legacy "PDB format" that has been used since nineteen-seventies. The details are shown in the Web page for the new standard format.

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.

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 ...

Download PDBETA

... folder/directory, PDBETA uses the information on secondary structure assignment in the PDB data. [1] W. Kabsch and C. Sander, Dictionary of protein secondary structure ...

News on 2014-7-9

Large Structures has been released" /> Improved Representation of Large Structures in the PDB Archive (wwPDB News)

News on 2006-02-27

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

The wwPDB is going to start to use a new standard format, PDBx/mmCIF in 2014, replacing the legacy \

The wwPDB is going to start to use a new standard format, PDBx/mmCIF in 2014, replacing the legacy "PDB format" that has been used since nineteen-seventies. The details are shown in the Web page for the new standard format.

[wwPDB] Poster Prize Awarded at IUCr

... . Individual sponsorships are also available. Consider supporting the next 50 years of PDB's spirit of openness, cooperation, and education with a donation to the ...

[wwPDB] Submit Abstracts for PDB50 by March 15

Throughout 2021, the wwPDB will be celebrating the 50th anniversary of the PDB archive (wwpdb.org/pdb50). The inaugural symposium will be held virtually on ...

News on 2007-04-25

The wwPDB (www.wwpdb.org) has collaborated on a project to remediate the PDB archive and create a new set of corrected files, the test data of which are now released.

Explore wwPDB-standardized electron density maps via PDBj EDMap

... files are available from our FTP site (ftp://ftp.pdbj.org/pub/pdb/validation_reports/) along with the validation reports. In addition, users can also ...

We'll finish to provide the PDBMLplus from FTP site. The default URL of PDBMLplus was changed in jV version 4.4 for this change.

... created by adding extra information collected by PDBj into PDBML-noatom (canonical PDB data file with XML format without atom coordinates), in following two manners ...

[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 ...

News on 2007-05-21

PDBj has started the following two new services: EM Navigator, a browser for searching the electron microscopy structures and XQuad (XQuery Advisor), a advisory tool for creating XQuery for searching the PDB data.

Educational Service

... S, Zardecki C, Voigt M, Berman HM, Burley SK (2015) The RCSB PDB “Molecule of the Month”: Inspiring a Molecular View of Biology. PLoS Biol ...

[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 ...

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 ...

Protein Data Bank 50th Anniversary Virtual Issue: Featured structural articles from The Journal of Biochemistry were released

... (JB). In this virtual issue, we celebrate the 50th anniversary of the PDB by highlighting the top 10 articles with higher citation numbers and the ...

[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.

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 ...

[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] Small Angle Scattering News

... aimed to test and benchmark different approaches for modeling SAS profiles from PDB coordinates has been published: A round-robin approach provides a detailed assessment ...

Previous workshop

... , September 27, 2014 1. "Modifications to the Protein Data Bank: A new PDB format, Data Deposition, and Validation Report" Genji KURISU (Institute for Protein Research ...

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