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News on 2004-04-13

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

News on 2011-04-13

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

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.

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 ...

News on 2011-06-17

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

EDM viewer

... together with molecular models. The EDMap viewer is integrated into the Mine PDB Entry Explorer via a link in the Database Information panel. Clicking on ...

[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] 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 ...

eF-surf

... and molecular surface of proteins from the atomic coordinate of proteins in PDB format. The electrostiatic potentials are calculated by solving the Poisson-Bolzman equation ...

[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 ...

eF-seek

... for the similar ligand binding sites for the uploaded coordinate file with PDB format. The representative binding sites in eF-site database are searched by ...

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 ...

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.

IPR seminar : PDBj-BINDS joint workshop on January 30, 2020

... interactions. The workshop provides PC-practices for compound-protein 3D data in PDB (Kawabata), comparisons of protein 3D structures (Rozewicki & Standley), and drug target database ...

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 ...

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 ...

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 ...

News on 2014-12-24

... based on user feedback. As a result of this successful release, RCSB PDB and PDBj will only accept depositions of structures determined from X-ray ...

News on 2014-7-9

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

News on 2015-1-27

... a result of this successful release, ADIT has been retired at RCSB PDB and PDBj for new depositions of structures determined from X-ray crystallographic ...

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 ...

confidentiality of deposition data - FAQ

... there any chance that the deposited information could leak out from the PDB before release? A) The deposited data is managed under strict security constraints ...

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 ...

A fasta file for all the sequence information is now available from the PDBj ftp site.

In addition to fasta sequence information ('fasta_seq_data/PDBID_seq.txt') for each PDB entry, a fasta file for all the sequence information ('all_fasta_sequence.txt.gz') is now available from the PDBj ftp site.

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