Data Exploration Services

"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

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.

UniProtKB Entries with Known 3D Structure

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.

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.

Video still from Tutorial 1 – Introduction to Visualization with Mol*

Mol* (molstar) is a modern, web-based open-source toolkit for visualization and analysis of large-scale molecular data. Mol* is used throughout RCSB.org, from generating the 2D images available for every structure and entity in the PDB; to offering interactive 3D views of structures, sequence annotations on structures, electron density; and close-up views of ligand interactions.

A standalone version of Mol* is also available that allows users to upload custom files and/or superimpose different structures in the same viewer.

To learn more about Mol* at RCSB.org:

• Introduction to Mol* Video Tutorial Series at PDB-101
• Documentation at RCSB.org
• Tutorials at Molstar.org

For an overview of Mol* features, see "Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures" Nucleic Acids Research (2021) 49: W431–W437 doi:10.1093/nar/gkab314.

Additional details about Mol* usage and development are available at Molstar.org.

With each weekly update, the PDB Data Distribution by Experimental Method and Molecular Type table is updated. Each number links to the corresponding set of structures.

These statistics are part of a large collection of PDB Statistics that offer interactive displays of data based upon different criteria. All statistics are generated using Web Services and represent the current holdings of the archive.

Data Distribution Table (as of June 1, 2022)

This snapshot also provides information about available experimental data files and structures with small molecule data.

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