Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures

Abstract

The Protein Data Bank Japan (PDBj, http://pdbj.org), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins. We herein outline the updated web user interfaces together with RESTful web services and the backend relational database that support the former. To enhance the interoperability of the PDB data, we have previously developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, which is now a wwPDB standard called wwPDB/RDF. We have enhanced the connectivity of the wwPDB/RDF data by incorporating various external data resources. Services for searching, comparing and analyzing the ever-increasing large structures determined by hybrid methods are also described.

Figure 1.

Basic web user interface. (A) On the PDBj home page, the user finds the main menu for all the services (on the left side of the page), interactive tutorials (top center) and service finder (in the middle). The omni-search bar (top left) guides the user to input keywords that are categorized into service types. (B) A search result is shown in several facets (PDB entries, ‘Info pages’, release status and chemical components) where the given keywords are found. (C) In the summary page of each PDB entry are shown basic information of the entry such as the title, authors, citation and validation report. Interactive molecular graphics are available for asymmetric units as well as biological units using Molmil (8) or JSmol (asymmetric units only) (http://wiki.jmol.org/index.php/JSmol) (right bottom).

Figure 2.

An example of PDBj Mine SQL queries. Queries can be executed on the web browser as well as via the RESTful web service (the database dump for local installation is also available). The result of a query can be saved in such formats as a custom XML, comma-separated values or tab-separated values. The plot on the right shows the yearly change of newly determined Pfam domains in the PDB, as obtained from a single SQL query against the PDBj Mine RDB. (Note that the data in the years 2015 and 2016 are incomplete because not all the PDB entries deposited in these years have been released yet.)

Figure 3.

Analysis tools for the PDB and EMDB. (A) The EM Navigator/Yorodumi (http://pdbj.org/emnavi) provides an integrated interface to the PDB and EMDB combined. (B) The Omokage search (http://pdbj.org/emnavi/omo-search.php) performs shape similarity searches through both the PDB and EMDB.