2021 PDBj web server transition

On 27-05-2021 we will transition our services to a new server, where we have worked on a renewed version of many of our services; some superficial, some extensive. A list of services that have been changed:

• Advanced Search has been merged with Quick Search
• A new "Search PDBj RDB" service is available, which is a graphical interface around our SQL service, to make it easier for users unfamiliar with SQL to search using any data part of the offical mmCIF and our pdbjplus data.
• The CIF-Query and XML-Query service have been discontinued, but the functionality has been integrated in our search system via the "Download results", where any arbitrary data category/item can be obtained from our RDB for the search matches in mmCIF, mmJSON or arbitrary JSON formats
• A new PDBj data archive has been prepared (https://data.pdbjbk1.pdbj.org/), where we have re-arranged our data files into a more logical and cleaned-up manner.
• The PDBMLplus format has been deprecated in favour for the mmJSON ones, which are available at https://data.pdbjbk1.pdbj.org/pdbjplus/data/cc/mmjson-plus/ and at each individual PDB entry page.
• The sequence navigator/neighbor interface has been renewed and the superposition functionality has been moved from the server-side using legacy PDB flat files to the client-side with Molmil using mmJSON files.
• The PDB entry page's Molmil interface (AU/BU) has been renewed.
• The EDMap Molmil interface has been renewed.
• eF-site has been integrated in the Mine PDB entry pages and the Molmil interface has been renewed.
• The Promode Elastic interface has been renewed.
• Our REST services have been renewed.
• Additional data has been added to our pdbjplus data (archive and files).
• The RDB delta files have been deprecated and replaced by our updater service

If you have any questions or comments, please contact us.