277 new PDB entries have been released on 2020-11-25.
277 new PDB entries have been released on 2020-11-25. 171588 entries are now available in total. Please refer to PDB / EMDB latest information for other updates.
The number of PDB entries processed by PDBj has reached 40,000
PDBj started processing PDB entries from July 2000, and the total number of PDB entries processed by PDBj since then has reached 40,000 in November 2020( Deposition statistics at wwPDB site ). Since the global number of PDB entries processed jointly by ...
[wwPDB] PDB Turns 49
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 ~170,000 structures of proteins, nucleic acids, and complex assemblies that ...
Explore wwPDB-standardized electron density maps via PDBj EDMap
PDBj now only provides the wwPDB calculated electron density maps through our EDMap service, where we previously used our own generated map data. From 2020-09-23, all legacy ED Map entries have been replaced by the wwPDB-standardized ED maps calculated ...
[wwPDB] Updated Validation Reports for Released PDB Structures
Updated validation reports for all X-ray, NMR, and 3DEM structures released in the PDB archive are now available. The updates include new percentile statistics reflecting the state of the PDB archive on December 31, 2019 and calculated map coefficients ...
Support Fund for Protein Data Bank Japan
Donation to this project Protein Data Bank Protein Data Bank (PDB), a database that archives the 3D structural information of biomacromolecules determined by experimental methods, started in 1971 with seven entries in the United States. In the latter ...
NMR Unified data
NMR-STAR is the official wwPDB format for storing NMR data, supported by an extensive dictionary [ GitHub ; Ulrich, E. L. et al. (2019) NMR-STAR: comprehensive ontology for representing, archiving and exchanging data from nuclear magnetic resonance ...
[wwPDB] Access Improved Carbohydrate Data at the PDB
A new data representation for carbohydrates in PDB entries and reference data improves the Findability and Interoperability of these molecules in macromolecular structures. The PDB archive now reflects: Standardized Chemical Component Dictionary ...
We will remove the data files of the previous version of the PDBj Mine RDB from our FTP site
We will remove the old data files for the previous version of PDBj Mine, which was retired in 2014, from our FTP site on July 29, 2020. We will continue to offer the data of our current PDBj Mine 2 RDB on ftp://ftp.pdbj.org/mine2/ . Mine 2 RDB also ...
2020 July is the 20th anniversary of PDBj.
Protein Data Bank Japan (PDBj) is celebrating the 20th anniversary in July, 2020. It was July 6th, 2000 when PDBj locally processed the 1st deposition to Osaka University, as a part of the JST-BIRD project. While in 2000, only 157 entries were processed ...
[wwPDB] Coming July 29: Improved Carbohydrate Data at the PDB
PDB data will incorporate a new data representation for carbohydrates in PDB entries and reference data that improves the Findability and Interoperability of these molecules in macromolecular structures. In order to remediate and improve the representation ...
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 ...
171588
PDB entries from 2020-11-25