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A paper describing PDBj's new tools and activities published in Protein Science.
New tools and functions in Data-out activities at Protein Data Bank Japan (PDBj)
Kinjo, A.R., Bekker, G.-J., Wako, H., Endo, S., Tsuchiya, Y., Sato, H., Nishi, H., Kinoshita, K.,
Suzuki, H., Kawabata, T., Yokochi, M., Iwata, T., Kobayashi, N., Fujiwara, T., Kurisu, G. and Nakamura, H.
Protein Science 27 (1): 95-102 (2018)
The new version of the Mine2 RDB has been released.
Please download the dump files for the new cc, ccmodel and prd. The delta files will be available from next week. Please also refer to RDB help page.
[wwPDB] Overview of PDB Validation Reports published in Structure
Individual Chemical Component Dictionary files (in mmCIF and PDBML) are now available at PDBj's FTP archive.
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[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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See the wwPDB news for more details.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 |
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Place | Kurokami North Campus, Kumamoto University Room I (Room E305 , General Education Bldg. 3F) |
number of seats | 100 |
<Presenter・Title>
-
Genji KURISU (Institute for Protein Research (IPR), Osaka University)
"Recent activities of PDBj and wwPDB" -
Akira KINJO (Institute for Protein Research (IPR), Osaka University)
"Querying the PDBj Mine2 relational database" -
Hirofumi SUZUKI (Institute for Protein Research (IPR), Osaka University)
"Situation, utilization and visualization of cryo-EM structure data"
※ Please take a numbered ticket (first come, first served) ahead at the reception counter on the day.
[wwPDB] PDB-Dev: A Prototype System for Integrative/Hybrid Structural Models announced in Structure
[wwPDB] Poster Prize Awarded at IUCr 2017
PDBj Format conversion service now supports Chem Comp file.
[wwPDB] wwPDB Events at IUCr (August 21-28)
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Visit the website (http://jbioinfo.jp/) for more detail.
[wwPDB] 5 Easy Steps to PDB Deposition
[wwPDB] Freezing the PDB Format
[wwPDB] Enriched PDB Structure Entry Files Conforming to OneDep Data Standards Are Now Available for Testing
[wwPDB] Revise Your Structure Without Changing the PDB Accession Code and Related Changes to the FTP Archive
[wwPDB] Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive
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.
Impact of PDBx/mmCIF v5 upgrade on PDBj services
Mine 2 RDB | Because all entries have been modified, the weekly delta file would be huge and will for that reason NOT be provided on the 12th. The delta files from the previous weeks will also no longer be included on the FTP. Delta files will be included again in the following week onwards (19th). Users will have to delete the current contents of the RDB and then download and load the full dump file, as described on the RDB help page. |
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Legacy PDBj Mine | Legacy PDBj Mine will no longer be updated after the transition of the PDBx/mmCIF dictionary from version 4 (v4) to version 5 (v5) planned on July 12, 2017. After this date, please use the new interface for PDBj Mine that will be compatible with the v5 data. The legacy PDBj Mine will be closed at the end of August, 2017. |
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 via the omni search, advanced search or the SQL search.Similarly, the dump files of the RDB on the FTP have also been updated. In case you experience any issues updating your local RDB with the delta file, please use the full dump file to upgrade the RDB as described on the RDB help page.