The PDB was announced on October 20, 1971 in Crystallography: Protein Data Bank Nature New Biology 233: 223 (1971) doi: 10.1038/newbio233223b0. Today, the PDB archive contains >180,000 structures of proteins, nucleic acids, and complex assemblies that ...

The symposium At the Cutting Edge of Structural Biology in Asia and Protein Data Bank's 50 Years of History will be held virtually on November 24. Register by November 8(JST) for the virtual symposium [ wwPDB News ]

Congratulations to biocurators Dr. Sutapa Ghosh and Dr. Monica Sekharan on processing over 10,000 PDB depositions. They are the second and third biocurators to reach this milestone. Yumiko Kengaku reached this milestone in April 2021. Dr. Ghosh received ...

PI name, email, and ORCiD ID will be publicly available in PDBx/mmCIF data files starting September 24, 2021 wwPDB continues to support research, education, and drug discovery worldwide. Open access to PDB data has helped researchers in structure- ...

Individual Chemical Component Dictionary entries and new archive inventory lists are now available for download Improved access to small molecule definitions (New tree: /pdb/refdata/) Individual Chemical Component Dictionary (CCD) and Biologically ...

In commemoration of PDB's 50 year anniversary, "PDB Asia 50 Anniversary Symposium - At the Cutting Edge of Structural Biology in Asia and Protein Data Bank's 50 Years of History -" will be held with the following contents. Date November 24, 2021 (Wed) * ...

CC0 1.0 Universal (CC0 1.0) Public Domain Dedication wwPDB manages the PDB Core Archives as a public good according to the FAIR Principles. In support of the FAIR objectives, wwPDB has replaced its historical data access license with a standard open ...

A special WEB site and movies for Coronavirus 3D structure are now available. These resources are developed for the exhibition for young students called “Web Science Fiesta 2021”. The title of the resources is “Shapes of proteins for living things – ...

From February 9, 2022, the wwPDB EMDB Core Archive will exclusively support version 3 of its data model and retire version 1.9.6 header files from the archive. The switch will involve several changes regarding file provision by the archive and this article ...

Coinciding with the release of our updated PDBj Mine service on May 27 2021, we also released a new PDBj data archive at data.pdbj.org, thus we have a total of three archives together with ftp.pdbj.org and ftp-versioned.pdbj.org. From September 1st 2021 ...

Journals, PDB users, and software developers should review code and begin to prepare for the change in format of PDB IDs and inclusion of PDB DOIs in PDBx/mmCIF files wwPDB, in collaboration with the PDBx/mmCIF Working Group, has set plans to extend ...

wwPDB continues to support research, education, and drug discovery worldwide. Open access to PDB data has helped researchers in structure-guided discovery and development of anti-coronavirus drugs, vaccines and neutralizing antibodies. When researchers ...

The Electron Microscopy Data Bank (EMDB), the public repository for electron cryo-microscopy maps and tomograms of macromolecular complexes and subcellular structures, is now an official partner in the Worldwide Protein Data Bank (wwPDB) collaboration ...

Poster Prize awardees At the inaugural PDB50 meeting, ~275 posters were presented (Abstracts Day 1 | Day 2); 209 of these presentations were considered for poster prize awards. - Best in High School: Nicholas Mamisashvili, Shelter Island High School ...

wwPDB validation reports are now provided in PDBx/mmCIF format for all new depositions in OneDep. This change makes validation data more interoperable with the PDB archival format. Data are more logically and better organized in the PDBx/mmCIF reports, and ...

The PDBj website has been updated due to transition to a new server. Please see the past news about the modifications of our services. If you have any questions or comments, please contact us.

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 ...