The PDBe-KB Aggregated Views of Proteins (https://pdbe-kb.org) have enabled our users to easily access collated structural and functional data from the whole PDB archive for their protein of interest. Thanks to recent updates, these pages are even faster and offer more opportunities to view the data in 3D with the Mol* viewer. To try out these new features now, visit pdbe-kb.org/proteins or visit an example page of Human MDC1.
Highlights:
- New, improved layout with more 3D interactivity
- New annotations
- Displaying predicted models
- Downloadable superposition data
The latest version of these Aggregated Views features a complete redesign of the page layout that aims to improve the performance of these pages. Instead of a single page, the sections are now divided into subpages, allowing us to add more data while also improving loading times. We also replaced the static images of structures on the “Summary� and “Structures� pages with the interactive 3D viewer, Mol*. You can navigate to these subpages using the navigation bar at the top of the screen and by clicking on the summary buttons on the landing page:
PDBe-KB is a collaborative consortium that provides a platform for data resources and scientific software developers to share valuable functional and biophysical annotations of protein and nucleic acid structures. Now, even more functional and biophysical annotations are available for view and download from the Aggregated Views of Proteins:
- Solvent accessible surface area per each PDB residue, provided by POPScomp and 3DComplex
- Molecular channels, provided by ChannelsDB
- Topology annotations, provided by KnotProt
- Post-translational modification annotations, provided by Scop3P
In addition to displaying all the structures available for a protein of interest from the whole PDB archive, we have integrated data from the to display any predicted structures available from model providers such as , , and . Users can view these structures in the interactive Mol* 3D viewer on the “Structures� subpage, by clicking on the grey boxes in the sequence feature viewer, ProtVista, for example, /pdbe/pdbe-kb/proteins/P01308/structures:
Our last major update of the Aggregated Views introduced the display of superposed structural clusters and superposed ligands. We now also provide access to the underlying data, such as the dendrograms the clustering is based on and the superposition matrices generated by the GESAMT tool. You can access these data on the , and by clicking on the “Superposition data and clustering dendrograms are available here� link at the top of the structural superposition views:
We designed these changes to improve the user experience of the Aggregated Views, allowing you to find relevant data to support their research more efficiently. We are continually improving our services to help the needs of our users - if you have suggestions for feedback, please use the “Feedback� option at the top of any PDBe or PDBe-KB page.
