The wwPDB has rolled out updated Chemical Component Dictionary (CCD) data files with standardized atom naming and additional annotation of protein backbone and terminal atoms within peptide residues. Entries containing those updated CCDs have been updated ...

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The wwPDB Foundation made awards to outstanding student posters at the 26th General Assembly and Congress of the International Union of Crystallography (IUCr) in Melbourne, Australia from August 22-29. Akila Pilapitiya Liliana Guerrero ...

A total of 268 structure entries deposited to PDB in a non-standard coordinate frame or space group setting have been re-versioned and re-released between December 2022 and September 2023. The updates have been made to enable improved model visualization ...

At the beginning of October 2023, the Electron Microscopy Data Bank (EMDB) will start distributing electron microscopy (EM) metadata for its entries in PDBx/mmCIF file format alongside the already available XML formatted files. The addition of PDBx/mmCIF ...

At current growth rates, we anticipate running out of three-character Chemical Component IDs by the end of 2023. After this point, the wwPDB will issue five-character alphanumeric accession codes for CCD IDs in the OneDep system. To avoid confusion with ...

wwPDB is celebrating its 20th anniversary. Meet wwPDB members from around the globe at the 26th General Assembly and Congress of the International Union of Crystallography (IUCr) in Melbourne, Australia from August 22-29. Visit the wwPDB booth #26 ...

In October 2023, the wwPDB will roll out updated Chemical Component Dictionary (CCD) data files with standardized atom naming and additional annotation of protein backbone and terminal atoms within peptide residues. Entries containing those updated CCDs ...

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The Worldwide Protein Data Bank celebrates its 20th anniversary in 2023 In July 2003, the Worldwide Protein Data Bank was launched as a partnership between RCSB Protein Data Bank (RCSB PDB, USA), Protein Data Bank in Europe (PDBe), Protein Data Bank ...

Version 1.0 of the next generation archive repository (NextGen) for the PDB archive was made available in early 2023. This “NextGen” archive hosts enriched atomic coordinate files, in both PDBx/mmCIF and PDBML formats, with files available to download at ...

Q) How can I submit a hybrid structure factor data with two datasets(x-ray/neutron)? A) You can generate a structure factor data with the following procedures. (original.mtz contains as follows; I-obs-xray SIGI-obs-xray R-free-flags-xray I-obs-neutron ...

NMR data files are standardized in NEF and NMR-STAR format [Ulrich, 2019] for the PDB entries which have NMR data in many different software specific formats. This remediation project provides unified NMR data in single NMR-STAR/NEF file for the PDB ...

With continuing growth of the PDB archive, the size of the file that lists all directory contents (currently https://files.wwpdb.org/pub/pdb/ls-lR) will become a challenge for long term maintenance. wwPDB plans to remove this file from the PDB archive at ...

The number of PDB depositions processed by PDBj during 23 years since we started has reached 50,000! This number corresponds to about 1/4 of all depositions. See also the press release (only in Japanese):

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With continuing growth of the PDB archive, the size of the file that lists all directory contents (currently https://files.wwpdb.org/pub/pdb/ls-lR) will become a challenge for long term maintenance. wwPDB plans to remove this file from the PDB archive at ...

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PDBj Newsletter Vol.23, which introduces recent activities of PDBj, has been released: English, Japanese

The wwPDB consortium would like to pay tribute to Dr. Olga Kennard OBE FRS upon the sad news of her passing. Her pioneering work on the development of crystallographic databases laid the groundwork for modern molecular structure data archiving and the ...

wwPDB, in collaboration with the PDBx/mmCIF Working Group, has set plans to extend the length of accession codes (IDs) for PDB and Chemical Component Dictionary (CCD) entries in the future. PDB entries containing these extended IDs will not be supported by ...

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An outcome of a project 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 of biomolecular small-angle scattering data reproducibility ...

A prototype of a next generation archive repository for the PDB is now available. The archive, called “NextGen”, hosts structural model files in PDBx/mmCIF and PDBML formats at files-nextgen.wwpdb.org. This enriched PDB archive provides annotation from ...