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

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

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

... 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 ...

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

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

... 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 ...

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

... 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 ...

... , 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 ...

... 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 ...

... 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 ...

... , 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 ...

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 ...

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.

... 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 ...

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 ...

On July 12 2017, the PDB entries in the FTP will be upgraded to the new v5 dictionary ( ...

... 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 ...

... 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 ...

... 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 ...

... .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 ...

... the initViewer JavaScript function (line 4) using PDBj's rest service for PDB entry files. Screenshot for page produced from the above code Alternatively, it ...

A new publication in Acta Cryst D announces the mandatory submission of PDBx/mmCIF to the PDB for crystallographic depositions. (wwPDB news)

... 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 ...