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 From 2020-09-23, all legacy ED Map entries have been replaced by the wwPDB-standardized ED maps calculated ...

Molecular viewer support In PDBj web site, we provide various molecular viewer pages. The available viewers for each web service is described below. Services Molecular Viewer jV Molmil Jmol JSmol PDBj Mine (PDB data browser) asymmetric unit ○ ○ ○ ...

[Introduction] The Electron Density Map (EDM) viewer allows the display of electron density maps together with molecular models. The EDMap viewer is integrated into the Mine PDB Entry Explorer via a link in the Database Information panel. Clicking on ...

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 ...

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 ...

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 ...

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 ...

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 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 includes ...

Advisors from the Scientific Community - Mitsuoka, Kaoru (Research Center for Ultra-High Voltage Electron Microscopy, Osaka University) - Kohda, Daisuke (Medical Institute of Bioregulation, Kyushu University) - Senda, Toshiya (Institute of Materials ...

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 ...

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 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 ...

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 ...

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 ...

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 【 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 research ...

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 ...

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 interactions ...