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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.

[wwPDB] Submit Abstracts for PDB50 by March 15

... May 4-5, 2021. The online sessions will take place between 11 a.m. – 4:30 p.m. ET each day. The event will be ...

[wwPDB] Celebrating 20 Years of the wwPDB

... 2023 In July 2003, the Worldwide Protein Data Bank was launched as a partnership between RCSB Protein Data Bank (RCSB PDB, USA), Protein Data Bank ...

[wwPDB] PDB Entries with Novel Ligands Now Distributed Only in PDBx/mmCIF and PDBML File Formats

... legacy PDB file format (see previous announcement). In addition, wwPDB has reserved a set of CCD IDs: 01 - 99, DRG, INH, LIG that will never ...

[wwPDB] ModelCIF Extension for Computed Structure Models

... , which is jointly managed by the worldwide Protein Data Bank (wwPDB) consortium. A software library called python-modelcif has been developed to support ModelCIF and ...

News on 2004-11-12

PDBj starts a new service in xPSSS to display the Electron Density Map of each biological macromolecule, whose structure factor file has been deposited, through the Summary page or the Experimental Details page of xPSSS.

[wwPDB] PDB NextGen Archive Now Provides Intra-molecular Connectivity

... file naming and data are structured based on extended PDB IDs with a two letter hash code, ‘third from last character' and 'second from last ...

Notice of Service Suspension (ASH, DASH, SeSAW, MAFFTash, Spanner, SFAS)

Due to a lack of IT personnel, the following services are now suspended. - ASH - DASH - SeSAW - MAFFTash - Spanner - SFAS

News on 2007-12-20

... have started to provide remediated PDB archive via rsync protocol. Rsync is a software which synchronizes files and directories from one location to another while ...

[wwPDB] Future Planning: Entries with extended PDB and CCD ID codes will be distributed in PDBx/mmCIF format only

... characters prefixed by ‘PDB’, e.g., pdb_00001abc. Each PDB ID has a corresponding Digital Object Identifier (DOI), often required for manuscript submission to journals ...

[wwPDB] Distribution of Electron Microscopy metadata in PDBx/mmCIF file format

... entries released before October 2023 will have PDBx/mmCIF files added at a later date. The description of PDBx/mmCIF categories and items featured in ...

[wwPDB] OneDep highlights curated assemblies for review in Mol*

... Mol* 3D viewer for depositors to review. This viewer is available in a new Review section in the deposition interface, which is present after curation ...

Remediation of Structure Factor Data and Release Plan

... in the archive for format consistency and correspondence with coordinate data. As a result, around 43,800 structure factor files have been updated to standardize ...

SFAS

... of the SFAS web service. The main reason for the suspension is a lack of IT personnel needed to perform security and data updates. If ...

EMDB header format to be updated to v.1.9.0

... .pdbj.org/pub/emdb/doc/XML-schemas/Header-schema/candidate/emdb.xsd . A complete list of changes can be found at the beginning of the ...

The new format, v.1.9.0, for the EMDB header file (XML file associated with each map) has been released

... .pdbj.org/pub/emdb/doc/XML-schemas/Header-schema/current/emdb.xsd A complete list of changes can be found at the beginning of the ...

Spanner

... of the Spanner web service. The main reason for the suspension is a lack of IT personnel needed to perform security and data updates. If ...

SeSAW

... of the SeSAW web service. The main reason for the suspension is a lack of IT personnel needed to perform security and data updates. If ...

MAFFTash

... of the MAFFTash web service. The main reason for the suspension is a lack of IT personnel needed to perform security and data updates. If ...

[wwPDB] Biocurator Milestone: >10,000 Depositions Processed

... microscopy. He has joined PDB in 2010 and has established himself as a highly qualified professional with deep understanding of scientific data and various experimental ...

[wwPDB] Congratulations to Poster Prize Winners

... : Nicholas Mamisashvili, Shelter Island High School, Molecular Dynamics Simulation of 6PEY.pdb a Novel Mutation in the Enzyme Methylenetetrahydrofolate Reductase - Best in Undergraduate: Ijeoma Okoye ...

DASH

... of the DASH web service. The main reason for the suspension is a lack of IT personnel needed to perform security and data updates. If ...

[wwPDB] Coming Soon: PDB Entries with Novel Ligands Distributed Only in PDBx/mmCIF and PDBML File Formats

... /mmCIF and PDBML formats (see previous announcement). In addition, wwPDB has reserved a set of CCD IDs: 01 - 99, DRG, INH, LIG that will never ...

[wwPDB] Updated Validation Reports for Released PDB Structures

... /validation_reports/ (PDBe) - ftp://ftp.pdbj.org/pub/pdb/validation_reports/ (PDBj) A snapshot of the previous version on June 10th is archived at RCSB ...

[wwPDB] Biocurator Milestone: >10,000 Depositions Processed

... PDBj in the Protein Research Foundation, Osaka. She has established herself as a highly qualified professional with deep understanding of scientific data and various experimental ...

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PDB entries from 2024-07-17

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