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mmJSON files now available from our FTP

The mmJSON files previously accessible via our REST interface are now also accessible from our ftp site. For more information, please refer to our mmJSON help page.

mmjson

The PDBx/mmJSON file format is a JSON representation of the PDBx/mmCIF data developed by PDBj. The following services use the mmJSON format directly: - Mine PDB Explorer - Mine CIF Query service - Molmil - CIF tree tool Implementation details and PDBx/ ...

wwPDB/RDF

URL: http://rdf.wwpdb.org/pdb PDB/RDF is a collection of PDB data in the Resource Description Framework (RDF) format. The RDF format is the standard format for the Semantic Web. An ontology defined in the Web Ontology Language (OWL) is also provided for ...

[wwPDB] PDB Certified as a Trustworthy Data Repository

PDB Certified as a Trustworthy Data Repository (wwPDB news)

PDBj omni-search functionality

The new PDBj omni-search functionality allows you to more quickly find the resource or service you're looking for. While you're typing, PDBj searches through several of our databases for matches regarding your query: Searching for "ubi" using the PDBj ...

[wwPDB] Depositing a Structure? Include Your ORCiD

Depositing a Structure? Include Your ORCiD (wwPDB news)

[wwPDB] ORCIDs to become mandatory for OneDep contact authors

ORCIDs to become mandatory for OneDep contact authors (wwPDB news)

REST interface

Many services accessible via the new web interface work via a REST interface. This REST interface is publicly available for users. Examples are also available. The PDBj REST services are available under the /rest/ URL. Search API URLhttps://pdbj.org/ ...

Obtain the PDBID + ChainID (auth_asym_id) of the entries containing the sequence \

- Search - PDBj Mine - SQL Search - Get each value of PDBID+ChainID (auth_asym_id) for structure which includes both sequence "TVSFSWNKFVPKQPNMILQGDAIVTSSGKLQLNKVDENGTPKPSSLGR" and resouce species "Glycine max" (soybean) Search from here SELECT b. ...

[wwPDB] Improvements to Data Replacement Prior to Release; Privacy Policy Update

Improvements to Data Replacement Prior to Release; Privacy Policy Update (wwPDB news)

[wwPDB] Conclusion of ORI Misconduct Review Results in Obsoletion of PDB Structures

Conclusion of ORI Misconduct Review Results in Obsoletion of PDB Structures (wwPDB news)

Customizing the PDBj web interface

[Direct panel customization] PDBj's new web interface's home PDBj web interface features it's main menu on the left side of the page. Each category has now been split up with each category having it's own panel. The main menu remains unchanged for all ...

Interactive Tutorial Series

PDBj web interface offers various new and exciting features. One of these features are the interactive tutorials. These tutorials will guide you through the various function of PDBj web interface. Currently available interactive tutorials: An ...

PDBj website browser requirements

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, ...

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PDB entries from 2024-11-06

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