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Remediation of 3DEM Entries in the Protein Data Bank (wwPDB News)

AutoDep, ADIT-NMR and EMDep Deposition Systems Have Been Retired, Effective September 30th 2016 (wwPDB News)

News, Aug 31, 2016 - Yorodumi Docs" /> On 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions. See this page for details. News, Aug 31, 2016 - Yorodumi Docs

A paper regarding Molmil, a molecular viewer developed by PDBj, has been published.

wwPDB Validation Server Upgrade (wwPDB News)

PDBj has started a service to link each PDBID to the database for Intrinsic Disordered proteins, IDEAL, which is developed by Nagoya University group.

Please refer to wwPDB validation report FAQs at wwPDB site.

eProtS eProtS (Encyclopedia of Protein Structures) is a dictionary with pictures of the protein three-dimensional structures, for understanding the tertiary structures and the biological functions for several selected protein molecules that are ...

Announcement: Map Volume Deposition to EMDB Will Be Mandatory for PDB Depositions of 3DEM models Starting September 6th, 2016 (wwPDB News)

URL: https://sysimm.org/ash_service/ [About ASH] ASH (Alignment of Structural Homologs) is a structure alignment program that has been developed for PDBj. Earlier versions of ASH were written by Hiroyuki Toh[1]. The core alignment algorithm based on the ...

The RDF version of SIFTS is now available at our FTP site ftp://ftp.pdbj.org/RDF/sifts/. SIFTS provides various annotations of protein sequences in the PDB such as the Gene Ontology, taxonomy (biological species), structural classifications (SCOP and CATH ...

Deposit ORCID and Grant Information with PDB Data (wwPDB News)

Access to wwPDB and RCSB PDB websites (wwPDB News)

The PDBeta web service has terminated. Please download PDBeta application and use it in local. We'll continue to update it.

AutoDep Deposition System to Be Retired, Effective August 25th 2016. ADIT-NMR and EMDep Deposition Systems to Be Retired, Effective September 30th 2016. (wwPDB News)

Improved Worldwide Support for wwPDB Deposition, Validation, and Annotation (wwPDB News)

- [Introduction] - [How to Use] - [Support] - [Trouble Shooting] Molmil as a standalone web-based viewer (for user-supplied files) is available from https://pdbj.org/molmil2/. Alternatively, Molmil is also available as a local installable version (with ...

Designate Depositions for the CASP-12 Structure Prediction Competition (wwPDB News)

jV 4.5.1." /> PDBj announces the bug fix update of the molecular viewer jV 4.5.1. The difference from the previous version (4.5) is that the bug fix involved in writing static image into directories without permission.

New NMR and 3DEM Validation Reports for Archived PDB Structures (wwPDB News)

Ligand Validation Workshop Paper Published (wwPDB News)

In this page, we refer to basic usage of PDBj. [Search entries by PDB ID] If you know the PDB ID which you want to get information, you can use the PDBj Mine. The procedure is described below. 1. At the top of the page you can find a search field. 2. ...

PDB Deposition wwPDB deposition & annotation (D&A) system is a new deposition tool developed by the wwPDB partners. It supports X-ray, EM and NMR structures. wwPDB Deposition tool : http://deposit-pdbj.wwpdb.org/deposition/ (PDBj) ADIT-NMR ...

The PDBj Mine2 relational database (RDB) now integrates the summary data of SIFTS developed by PDBe and UniProt. By combining PDBj Mine2 and SIFTS, the user can easily retrieve, using SQL, various annotations of protein sequences in the PDB such as the ...