217 new PDB entries have been released on 2020-05-27.
217 new PDB entries have been released on 2020-05-27. 164391 entries are now available in total. Please refer to PDB / EMDB latest information for other updates.
We are waiting for donation to the PDBj donation window in the Osaka University Foundation for the Future
We established a PDBj dedicated donation window in the Osaka University Foundation for the Future. We are going to utilize the donated fund to enhance and improve the public relations activities that cannot be covered by research funds from the national ...
[wwPDB] An updated PDB-Dev website
An updated PDB-Dev website A new and improved PDB-Dev website is now available. PDB-Dev is a prototype system which helps wwPDB partners to understand the requirements in archiving integrative structures. It has been built based on recommendations from ...
Prize of the minister of MEXT in the science and technology field in 2020 was awarded
In 2000, we started the activity of Protein Data Bank Japan (PDBj) at Institute for Protein Research of Osaka University, and have managed the international Protein Data Bank collaborated with Europe and America. On 7th April 2020, the prize of the ...
[wwPDB] Streamlining of EMDB’s Map Entry Release Process
Beginning April 15th 2020, the Electron Microscopy Data Bank (EMDB) will end its practice of releasing map entry metadata (so-called XML header files) prior to release of the primary map and associated files. For new EMDB map depositions, this metadata ...
COVID-19 featured content has been relased.
PDBj has released the featured page containing all entries directly related to the Novel Coronavirus disease (COVID-19) which is a serious threat to people all over the world. 【COVID-19 featured content】 https://pdbj.org/featured/covid-19 【Molecule of ...
COVID-19 featured content
Coronavirus, 2020. Modified from the original illustration by David S. Goodsell@RCSB PDB The recent outbreak of the Novel Coronavirus disease ( COVID-19 ) is a serious threat to people all over the world. In order to understand and develop an effective ...
[wwPDB] Improving carbohydrates in the PDB for 2020
In July 2020, the wwPDB will roll out updated PDB structures and reference data files with standardized representation of carbohydrate molecules, improving the Findability and Interoperability of PDB data. Detailed information about this work is available ...
[wwPDB] Improve Your Previously-Released Coordinates AND Keep Your Original PDB ID: Phase II
We are pleased to announce that from February 18, 2020 authors (PIs) of released PDB structures can update the model coordinates while retaining the same PDB accession code, thereby preserving the link with the original publication. In this second and ...
[wwPDB] New Coronavirus Protease Structure Available
PDB data provide a starting point for structure-guided drug discovery A high-resolution crystal structure of 2019-nCoV coronavirus 3CL hydrolase (Mpro) has been determined by Zihe Rao and Haitao Yang's research team at ShanghaiTech University. Rapid ...
Launch of our renewed EDMap service
Today we have launched the renewed EDMap service. The new version of EDMap shows the recently introduced wwPDB Electron Density Coefficient Files for new entries. For legacy entries, the old data is used, but with a revised implementation that improves ...
What is the threshold to categorize as polymers for PDB entities? - FAQ
Q) The molecule type for each entity is defined in entity.type . So what is the threshold to categorize as polymers for PDB entities? A) Currently, peptides with three or more residues and nucleotides with two or more bases are defined as polymers. But ...
[wwPDB] Distribution of NMR data in a unified format at the PDB archive
The wwPDB partners are pleased to announce that as of March 2020 the OneDep system will begin accepting upload of NMR experimental data as a single file, either in NMR-STAR or NEF format. This will start the transition from the current practice where ...
[wwPDB] EMDB policy and procedures document now available
A comprehensive policy and procedures document for the EMDB archive has been drawn up by the EMDB team in order to ensure consistent and coherent rules for its data. The document is now available to view on the EMDB website . Since its foundation in 2002, ...
[wwPDB] Time-stamped Copies of PDB and EMDB Archives
A snapshot of the PDB Core archive ( ftp://ftp.wwpdb.org ) as of January 1, 2020 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 ...
IPR seminar : PDBj-BINDS joint workshop on January 30, 2020
IPR seminar : PDBj-BINDS joint workshop “Protein and Compound Structural Data for Drug Discovery and Life Science” Purpose Structural data for proteins and compounds are useful for drug design and life science to know mechanisms of molecular ...
CiCLE workshop: sample evaluation for cryo-EM on January 6 or January 7, 2020
CiCLE workshop: sample evaluation for cryo-EM Outline:For obtaining high-resolution structures by single particle cryo-EM suitable sample evaluation and sample preparation is essential. An important aspect of sample evaluation is the effective use of ...
[wwPDB] Additional EM map validation now available through OneDep
The wwPDB validation reports provided in the OneDep system now have additional validation for electron microscopy (EM) maps to help users identify potential discrepancies in their data. The updated wwPDB validation reports in the OneDep system now ...
[wwPDB] Improved resolution of DOIs for PDB entries
The wwPDB partners are pleased to announce an improved mechanism for the resolution of digital object identifiers (DOIs) associated with released PDB entries. We have launched new wwPDB landing web-pages for each released PDB entry. These pages present ...
PDBj Logo
The PDBj Logo is allowed to use freely as far as the purpose is related to PDBj (e.g. copyright notices, icons for linking to the PDBj web site such as PDB search results and PDB entry pages). Low resolution (529px × 181px, 72dpi, RGB, for screen) ...
Encyclopedia of Protein Structures (eProtS)
The service of Encyclopedia of Protein Structures (eProtS) is now under maintenance.
News Letter / Leaflet
Newsletter Latest (Vol.21, 6 pages) Japanese English Previous news letters are here . Leaflet for researchers (2 pages) Japanese English Leaflet for general people (6 pages) Japanese
On 24th Sep, we’ll hold a luncheon seminar at the Annual Meeting of the Biophysical Society of Japan in Miyazaki
On 24th Sep, we will hold a luncheon seminar at the 57th Annual Meeting of the Biophysical Society of Japan in Miyazaki. Details are the following: Date 24th September 2019 (Tue) 11:30 - 12:20 (JST) Venue Seagaia Convention Center, Room G (IVORY) ...
On 18th Aug (Sun), we exhibit a booth at the 29th Science Festa Osaka
We'll exhibit a booth at the 29th Science Festa Osaka , which is a scientific event for young people. The exhibition day of our booth is only on 8/18 (Sun). We are going to exhibit the following menus: Explanation of the basic for proteins Experience ...
[wwPDB] Improve your previously released coordinates AND keep your original PDB ID with OneDep
We are pleased to announce the availability of PDB versioning, allowing depositors to update their entries while retaining the same PDB accession code. Depositors can now submit new coordinates for existing entries. Initially, this is limited to PDB ...