In 2025, ~3.3 billion data files in various file formats, including atomic coordinate files, experimental data files, chemical and molecular reference data files, FASTA sequence files, and official wwPDB validation reports, were downloaded and/or viewed from RCSB PDB-hosted servers. Additional data were downloaded from wwPDB partners PDBe and PDBj, giving a global total of more than 4.7 billion data file downloads. 

RCSB PDB Internal Analytics reported that 6.3 million unique clients accessed RCSB.org over approximately 34 million sessions during the same time period.

RCSB PDB has released an updated Advanced Search interface to provide a cleaner, more intuitive experience while enhancing support for exploring 3D structures across both experimentally determined structures and Computed Structure Models (CSMs). Unlike the top-bar Basic Search, Advanced Search offers fine-grained control over which data fields to search, the type of search to perform, and how results are combined.

Advanced Search can query the PDB based on Structure Attributes, Sequence Similarity, Sequence Motif, 3D Similarity, and 3D Motif; RCSB PDB also offers Chemical Search and Browse Annotations tools.

3D Motif Search

Advanced Search now enables more efficient construction of complex queries, including 3D structural searches, along with seamless integration with interactive Mol* visualization. Users can select 3D structures (including chains, assemblies, or structural motifs) directly within the Mol* viewer for PDB structures, CSM entries, and user-uploaded coordinate files. Users can also select 3D motifs from a library of catalytic residues and build queries based on residues involved in ligand interactions.

Chemical Search

The redesigned Chemical Search identifies small molecules in the PDB archive that are similar to a particular query. Small molecules are defined in the wwPDB's Chemical Component Dictionary (CCD) and the Biologically Interesting Molecule Reference Dictionary (BIRD). Chemical Search uses an integrated interactive chemical drawing tool and supports metadata-based searches such as chemical name or molecular weight.

3D Structure Similarity Search

RCSB PDB's Structure Similarity Search has been redesigned to deliver faster and more scalable structural comparisons across experimentally determined and predicted Computed Structure Models (CSMs).

This new capability improves the accuracy and relevance of 3D Similarity search results on the RCSB.org website, helping users more effectively identify structurally related and distant homolog macromolecules.

The updated 3D similarity search uses machine learning–based embeddings to represent macromolecular structures in a high-dimensional vector space. Combined with vector databases, this approach enables efficient comparison of 3D structures at scale and improves sensitivity to 3D structural similarity, making it well-suited for exploring large collections of predicted models alongside experimentally determined structures.

For more on this feature, read the 3D Similarity Search help article and theSearch API reference.
For methodological details, see

Multi-scale structural similarity embedding search across entire proteomes
Joan Segura, Ruben Sanchez-Garcia, Sebastian Bittrich, Yana Rose, Stephen K Burley, Jose M Duarte (2026) Bioinformatics 42: btag058 doi: 10.1093/bioinformatics/btag058

RCSB.org offers access to PDB experimental structures, integrative structures, and Computed Structure Models (CSMs) from AlphaFold DB and ModelArchive.

Want to learn how to use RCSB.org features to navigate 3D predicted protein structures in the context of experimentally-determined PDB structure? Watch this demonstration video to learn how to use this powerful RCSB.org feature.
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Read how RCSB.org supports discovery, analysis, and visualization of integrative structures together with single-method experimental structures and CSMs.

RCSB Protein Data Bank: Delivering integrative structures alongside experimental structures and computed structure models
Brinda Vallat, Yana Rose, Dennis W Piehl, Jose M Duarte, Sebastian Bittrich, Chunxiao Bi, Joan Segura, Arthur Zalevsky, Monica R Sekharan, Benjamin M Webb, Charmi Bhikadiya, Maria Voigt, Jeremy Henry, Henry Chao, Aditya Pingale, David Raymond, Jared Sagendorf, Ezra Peisach, Zukang Feng, Vladimir Guranovic, James Smith, Alexander S Rose, Jasmine Y Young, Helen M Berman, Andrej Sali, Stephen K Burley
(2026) Nucleic Acids Research 54: D489–D498 doi: 10.1093/nar/gkaf1187