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On 27-05-2021 we will transition our services to a new server, where we have worked on a renewed version of many of our services; some superficial, some extensive. A list of services that have been changed: - Advanced Search has been merged with Quick ...

While the standard quick search only allows filtering on a selection of the metadata, the RDB Query Builder enables more flexible filtering of PDB/chem_comp/BIRD/EMDB entries using all the metadata included within the Mine 2 RDB. Note that for even more ...

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

pdb-l@lists.wwpdb.org is an open discussion forum for questions and discussions with the PDB user community about protein structure, analysis, and related topics. Messages sent to pdb-l@lists.wwpdb.org will be sent to all subscribers. This bulletin board, ...

Congratulations to wwPDB’s Ms. Yumiko Kengaku on processing 10,000 depositions. Yumiko began her career as a biocurator in 2000, as a member the newly-formed PDBj team at her alma mater Osaka University. She is the 1st wwPDB biocurator to process more than ...

In October 2020, a subgroup of the wwPDB PDBx/mmCIF Working Group was convened to develop a richer description of experimental data and associated data quality metrics. Members of this Data Collection and Processing Subgroup are all actively engaged in ...

To improve the clarity of assembly definitions in curation, wwPDB now makes curated PDB assemblies available for depositors to view in OneDep using the Mol* viewer. One of the important processes in curation of PDB entries is the definition of ...

In 2014, PDBx/mmCIF became the PDB’s archive format and the the legacy PDB file format was frozen. In addition to PDBx/mmCIF files for all entries, wwPDB produces PDB format-formatted files for entries that can be represented in this legacy file format (e. ...

A new article in Structure describes new features, including branched representations and 2D SNFG images for carbohydrates, identification of ligands of interest, 3D views of electron density fit, and 2D images of small molecule geometry. These ...

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 May 4-5, 2021. The online sessions will take place between 11 a.m. – 4:30 p.m. ET each day. ...

- Fifty years of Protein Data Bank in the Journal of Biochemistry Genji Kurisu The Journal of Biochemistry 171(1) 3-11 2022 10.1093/jb/mvab133 - Fifty years of Protein Data Bank in the Journal of Biochemistry - Genji Kurisu - The Journal of Biochemistry - ...

With this week's update, 1,018 SARS-CoV-2-related structures are now freely available from the Protein Data Bank. The first SARS-CoV-2 structure, a high-resolution crystal structure of the coronavirus main protease (PDB 6lu7), was released early in the ...

You can have a local copy of the Mine 2 Relational DataBase by using dump files provided by PDBj. The dump files have been designed to be used with a recent version of PostgreSQL. In the future we will also release a manager script to help install and ...

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 an event hosted by the American Society for Biochemistry and Molecular Biology and organized by the wwPDB ...

The wwPDB archive has now been updated to include validation reports for every released set of EM model coordinates in the PDB and every released EMDB map entry. Validation reports provide quantitative and visual assessments of structure quality and enable ...

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A snapshot of the PDB Core archive (ftp://ftp.wwpdb.org) as of January 5th, 2021 has been added to ftp://snapshots.wwpdb.org and ftp://snapshots.pdbj.org. Snapshots have been archived annually since 2005 to provide readily identifiable data sets for ...

The PDB was announced on October 20, 1971 in Crystallography: Protein Data Bank Nature New Biology 233: 223 (1971) doi: 10.1038/newbio233223b0. Fifty years later, the PDB archive contains >170,000 structures of proteins, nucleic acids, and complex ...

Newsletter Latest (Vol.24, 6 pages) - 日本語 English Previous news letters are here. Flyer for researchers (2 pages) - 日本語 English Leaflet for general people - 日本語 (A3 6 pages A4 12 pages) 2021 Calendar for celebrating 50th anniversary of PDB ...

An archival-level carbohydrate remediation project that led to the re-release of over 14,000 PDB structures in July 2020. This update includes diverse oligosaccharides: glycosylation; metabolites such as maltose, sucrose, cellulose fragments; ...

wwPDB validation reports provided in OneDep now include restraints validation for NMR entries to help users identify potential discrepancies in their data. Recommendations from the wwPDB NMR Validation Task Force (VTF) on how restraints data should be ...

- Head Kurisu, Genji, Ph.D. (Prof., IPR, Osaka Univ.) - Kurisu, Genji, Ph.D. (Prof., IPR, Osaka Univ.) - Group for Data-in of PDB/EMDB Nakagawa, Atsushi, Ph.D. (Prof., IPR, Osaka Univ.) Yu, Jian, Ph.D. (Assoc. Prof., IPR, Osaka Univ.) Cho, Hasumi (Chen, ...