The new version of the Mine2 RDB has been released. The new version includes Chemical Component(cc), Chemical Component Model(ccmodel) and BIRD molecule(prd) schema. The schema of the PDBj Mine 2 RDB has also been upgraded to pdbx-v50-v5.287. Please download the dump files for the new cc, ccmodel and prd. ... |
[wwPDB] Overview of PDB Validation Reports published in Structure Overview of PDB Validation Reports published in Structure (wwPDB news) |
Individual Chemical Component Dictionary files (in mmCIF and PDBML) are now available at PDBj's FTP archive. Individual Chemical Component Dictionary files (in mmCIF and PDBML) are now available at PDBj's FTP archive. For more details, please try Chemie search and chem_comp/RDF service. |
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Format Conversion: Do you provide a service to convert the file format between PDB format and PDBx/mmCIF? - FAQ Q) Format Conversion: Do you provide a service to convert the file format between PDB format and PDBx/mmCIF? A) By using our Format Conversion web service, you can convert the file format between PDB format and PDBx/mmCIF. [Back to the question list] |
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Previous workshop PDBj luncheon seminar at the 55TH ANNUAL MEETING OF THE BIOPHYSICAL OF JAPAN, September 21, 2017 - 1:Genji Kurisu (Institute for Protein Research (IPR), Osaka University) "Recent activities of PDBj and wwPDB" - 2:Akira Kinjo (Institute for Protein ... |
[wwPDB] Implementation of PDB Entry Versioning and Better Revision History to Improve PDB Archive Management Implementation of PDB Entry Versioning and Better Revision History to Improve PDB Archive Management (wwPDB news) |
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PDBj luncheon seminar at the 55th Annual Meeting of the Biophysical Society of Japan, September 21, 2017 <PDBj luncheon seminar> PDBj luncheon seminar will be held at The 55TH ANNUAL MEETING OF THE BIOPHYSICAL SOCIETY OF JAPAN . Date September 21 (Thu), 2017 11:45-12:35 Place Kurokami North Campus, Kumamoto University Room I (Room E305 , General ... |
[wwPDB] PDB-Dev: A Prototype System for Integrative/Hybrid Structural Models announced in Structure PDB-Dev: A Prototype System for Integrative/Hybrid Structural Models announced in Structure (wwPDB News) |
[wwPDB] Poster Prize Awarded at IUCr 2017 Poster Prize Awarded at IUCr 2017 (wwPDB News) |
Search 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 ... |
Services and Softwares Yorodumi Yorodumi is a website to easily watch, move, rotate, learn, and enjoy 3D structures of biological molecules. See Yorodumi Docs for more details. URL: https://pdbj.org//yorodumi/ |
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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) |