Data Query, Reporting, and Access

NGL Viewer user interface and surface rendering of "The Crystallographic Structure of Panicum Mosaic Virus" (4V99)

The new Pathway View provides a graphical representations of metabolic pathways. The color-coding indicates what parts of the pathway have been determined at atomic level resolution in PDB, inferred via homology models, or cannot be modeled right now.

• Fast, interactive display of molecular complexes containing millions of atoms is now possible, without plug-ins, on desktop computers and smartphones. The new NGL Viewer enables easy visualization of even the largest structures for everyone in research and education. In addition, the new binary compressed Macromolecular Transmission Format (MMTF.rcsb.org) massively reduces network transfer and parsing times. With these advances, we are prepared for upcoming advances in experimental techniques that are already delivering structures of rapidly increasing size and complexity.
• 3D structures of an increasing number of proteins that perform reactions within metabolic pathways are available in the PDB. To accommodate a deeper structural view of biology, the new Pathway View allows users to browse through well-characterized metabolic pathways and access the corresponding PDB entries.
• Text searching from rcsb.org for RCSB PDB news and PDB-101 content has been enabled. Simply enter a keyword term in the top search box (upper right hand corner of every page) and hit enter. Matching content will be returned in the "News & PDB-101 Articles" tab, including Molecule of the Month, Educational Resources, and images from the Irving Geis Digital Archive.
• Several resources that store diffraction image data related to PDB structures have been recently established. These data are made available to help improve the reproducibility of experiments and the automation of structure determination tools. Using Digital Object Identifiers (DOIs), more than 2,800 sets of diffraction image data available from the Integrated Resource for Reproducibility in Macromolecular Crystallography (ProteinDiffraction.org) have been connected to PDB entries. Links to diffraction image data from The Structural Biology Data Grid are already available.
• Protein Modifications in the PDB have been mapped to the RESID database of Protein Modifications and the associated Protein Modifications Ontology (PSI-MOD). Explore these modifications with the new Protein Modification Browser, Advanced Search, and the 3D View and Sequence options on Structure Summary pages. A detailed overview is available.
• Biological assembly files for large structures are now available in PDBx/mmCIF format from Structure Summary pages. The biological assembly is the macromolecular assembly that has either been shown to be or is believed to be the functional form of the molecule. The PDBx/mmCIF format has no restrictions on the number of atoms and chains and can hold biological assemblies of any size. For more information, see PDB-101’s biological assembly tutorial. Download these data files from each Structure Summary page.

Access from the http://rcsb.org website to PDB model coordinate and experimental data files and small molecule data files now occurs via the HTTPS (“secure”) protocol. No changes need to be made as the website has been updated to use HTTPS wherever possible.

Additionally, the entire PDB-101 educational website is served via HTTPS.

RCSB PDB HTTPS services will continue to expand over the next few months. For ongoing technical updates, visit http://status.rcsb.org or subscribe to our Status Update mailing list.