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PDBj website implements cutting-edge technology. To make full use of our web interface, we recommend users to use the latest version of the most commonly used browsers and have JavaScript enabled. The latest version of browsers provide users with new ...

[wwPDB] Protein Structures Sought for CASP13

Protein Structures Sought for CASP13 (wwPDB news)

[wwPDB] Access Updated Validation Reports for PDB Structures

Access Updated Validation Reports for PDB Structures (wwPDB news)

PDBj Mine

PDBj Mine is a web interface to search the PDB. PDBj Mine has the following basic features: 1. PDBj Mine is based on a relational database. 2. Allows enhanced keyword search. 3. Detailed queries can be performed using using SQL. - PDBj Mine:SQL ...

[wwPDB] wwPDB Biocuration Highlighted in New Publication

wwPDB Biocuration Highlighted in New Publication (wwPDB news)

The new version of jV was released (4.5.4)

We announce the new version of jV, Java based molecular viewer, was released. The latest version is 4.5.4. There is no functional change compared to the previous version. Only the certification for signing was updated. In some cases update procedure is ...

eF-surf

eF-surf is a web service to calculate the electrostatic potential and molecular surface of proteins from the atomic coordinate of proteins in PDB format. The electrostiatic potentials are calculated by solving the Poisson-Bolzman equation numerically. ...

eF-seek

eF-seek is a web server to search for the similar ligand binding sites for the uploaded coordinate file with PDB format. The representative binding sites in eF-site database are searched by our own algorithm based on the clique search algorithm. eF-seek ...

[wwPDB] Time-stamped Copies of the PDB Archive Available

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

PDBj FTP site (PDB Archive) is available via \

The PDB Archive download service is now available via the http protocol in addition to ftp and rsync. - http://ftp.pdbj.org/ (current main PDB Archive) - http://ftp-versioned.pdbj.org/ (versioned PDB Archive) *Please see also "About contents in PDBj ...

A paper describing PDBj's new tools and activities published in Protein Science.

http://onlinelibrary.wiley.com/doi/10.1002/pro.3273/full 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., ...

eF-site

About eF-site eF-site (electrostatic-surface of Functional site) is a database for molecular surfaces of proteins' functional sites, displaying the electrostatic potentials and hydrophobic properties together on the Connolly surfaces of the active sites, ...

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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Tutorial for OneDep deposition service - FAQ

Q) Is any tutorial for OneDep deposition service available? A) Please refer to tutorial page at PDBj site. Other information regarding deposition is provided at Data Deposition Information page. [Back to Questions]

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)

[wwPDB] Donate Today to Support the PDB's Spirit of Openness, Cooperation and Education

The wwPDB Foundation raises funds from Individual and Corporate sponsors in support of the outreach activities of the wwPDB crucial to the future of the PDB archive, including workshops, symposia, and advisory meetings. 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 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)

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