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PDB entry search (PDBj Mine) PDBj Mine is a new generic interface to search PDB entries by PDB ID and keyword etc. See also Basic Usage. URL: http://pdbj.org/mine/ Advanced Search (PDBj Mine) In Advanced Search, you can use combination of ...

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PDBj Format conversion service now supports Chem Comp file.

PDBx/mmCIF Conversion service provided by PDBj now supports Chemical Component files in mmCIF format. The Chem Comp file in mmCIF format is converted to PDB format file.

[wwPDB] wwPDB Events at IUCr (August 21-28)

wwPDB Events at IUCr (August 21-28) (wwPDB News)

Rest interface examples

Example of curl An example of the curl command used in UNIX like systems to get structural data file of HEM chemical component in the mmCIF format. $ curl -F "id=HEM" -F "format=mmcif" https://pdbj.org/rest/downloadCOMPfile > HEM.cif.gz % Total % ...

[wwPDB] Better Management of PDB Archive with File Versioning and Revision History

Better Management of PDB Archive with File Versioning and Revision History (wwPDB News)

JBI (Japan alliance for Bioscience Information) portal site is now open.

PDBj has launched the JBI (Japan alliance for Bioscience Information) portal site (http://jbioinfo.jp/) in collaboration with National Bioscience Database Center (NBDC)/JST, Database Center for Life Science (DBCLS)/Joint Support-Center for Data Science ...

[wwPDB] 5 Easy Steps to PDB Deposition

5 Easy Steps to PDB Deposition (wwPDB News)

[wwPDB] Freezing the PDB Format

Freezing the PDB Format (wwPDB News)

[wwPDB] Enriched PDB Structure Entry Files Conforming to OneDep Data Standards Are Now Available for Testing

Enriched PDB Structure Entry Files Conforming to OneDep Data Standards Are Now Available for Testing (wwPDB News)

[wwPDB] Revise Your Structure Without Changing the PDB Accession Code and Related Changes to the FTP Archive

Revise Your Structure Without Changing the PDB Accession Code and Related Changes to the FTP Archive (wwPDB News)

[wwPDB] Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive (wwPDB News) Impact on PDBj services Mine2 RDB was upgraded to pdbx-v50-v5.282. Please refer to the past news regarding impact of V5.0 upgrade on PDBj services ...

CIF --> JSON converter

This tool can load a PDBx/mmCIF file and convert it to PDBx/mmJSON. Besides PDBx/mmCIF, other STAR formatted files should also work. Select a file below and then click on "Convert". Note that the files will not be uploaded to the server, but will be ...

Impact of PDBx/mmCIF v5 upgrade on PDBj services

On July 12 2017, the PDB entries in the FTP will be upgraded to the new v5 dictionary ( http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) (wwPDB News). Since this will be a major upgrade, some services will be affected. The following services ...

PDBMLplus schema file

About PDBMLplus PDBMLplus_v40.xsd (XML Schema) Display (3.55MB) Download (gzipped 297KB) PDBMLplus_v42.xsd (XML Schema) Display (3.55MB) Download (gzipped 297KB) View with tree viewer

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Using PDBj's web-interface

The new PDBj web interace offers users a bleeding edge web application designed for the future. Software requirements A wide range of browsers are supported. For feature and performance reasons, we recommend you to use the latest version of the following ...

News on 2017-4-19

The schema of the PDBj Mine 2 RDB was upgraded to pdbx-v42-v4.069. On 2017-04-19 the schema of the PDBj Mine 2 RDB was upgraded to pdbx-v42-v4.069, adding support for new tables such as pdbx_deposit_group, enabling searching for group deposition IDs either ...

Archival PDBx/mmCIF Version V4 to V5 Update in the Protein Data Bank ( wwPDB News )

Archival PDBx/mmCIF Version V4 to V5 Update in the Protein Data Bank (wwPDB News)

Updated Validation Reports for Archived PDB Structures Now Available ( wwPDB News )

Updated Validation Reports for Archived PDB Structures Now Available (wwPDB News)

Data Management: A global coalition to sustain core data ( wwPDB News )

Data Management: A global coalition to sustain core data (wwPDB News)

The paper describing wwPDB OneDep system is now available ( wwPDB News )

The paper describing wwPDB OneDep system is now available (wwPDB News)

Time-stamped Copies of the PDB Archive Available ( wwPDB News )

Time-stamped Copies of the PDB Archive Available (wwPDB News)

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PDB entries from 2024-04-17

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