News

New Ways to Explore Similar Proteins

05/09

"Group" summary pages and search results simplify exploration of PDB structures with similar sequence identity/UniProt ID or were deposited as part of the same study"Group" summary pages and search results simplify exploration of PDB structures with similar sequence identity/UniProt ID or were deposited as part of the same study

The PDB archive contains many entries that are very similar:

Structures: Some structures were deposited to the PDB together at the same time using the RCSB PDB Group Deposition server. These collections of structures (e.g., structures with same protein/s, but different bound ligands) are assigned a Group Deposition ID that identifies the collection.

Polymer Entities: Multiple PDB entries will contain polymer entities that share similar sequence identity (from 100% to 30%) as well as entities with the same UniProt Accession ID.

New features can be used to explore these "groups"

  • Advanced Search return option can be used to detect similarity among search results and return data in "grouped" sets.

  • Group Summary Pages provide overviews of key features, properties, sequence alignments, and annotations of any predetermined or custom group.

  • Additionally, an interactive chart highlights the growth by year of unique UniProtKB sequences with known 3D structure.

    • Advanced Search

    Advanced Search options for displaying similar results as a "group" containing multiple entities/structures or as "representative" example.Advanced Search options for displaying similar results as a "group" containing multiple entities/structures or as "representative" example.

    Grouped search results will highlight the number of structures in a group along with related information (example).

    Access detailed documentation about this new feature for grouping redundant search results.

    Group Summary Pages

    Access group summary pages to explore similar entities or structures.Access group summary pages to explore similar entities or structures.

    UniProtKB Entries with Known 3D Structure

    PDB Statistics: UniProtKB Entries with Known 3D Structure (Annual)PDB Statistics: UniProtKB Entries with Known 3D Structure (Annual)

    This chart shows the total number of unique UniProtKB entries in PDB structures released within each year. It is updated weekly.

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