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RCSB protein data Bank: Next-generation advanced search for exploration of experimental structures and computed
Yana Rose1, Ronald Brown2, Maria Voigt2
1Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center; University of California, La Jolla, California, USA.
Protein Science : a Publication of the Protein Society
|July 28, 2026
Summary
The Protein Data Bank (PDB) now offers redesigned Advanced and Chemical Search tools for intuitive discovery of 3D macromolecular structures and chemical diversity. These tools enhance exploration of structure-function relationships for a diverse scientific community.
Area of Science:
- Structural Biology
- Bioinformatics
- Computational Chemistry
Background:
- The Protein Data Bank (PDB) is a crucial archive for experimentally determined 3D macromolecular structures.
- RCSB.org provides access to PDB data and over a million predicted structures.
- Increasing data volume necessitates improved search capabilities for the scientific community.
Purpose of the Study:
- To describe a redesigned Advanced Search capability for the RCSB.org web portal.
- To enhance the discovery of 3D macromolecular structures and chemical entities.
- To facilitate exploration of structure-function relationships.
Main Methods:
- Integration of annotation-, sequence-, and 3D structure-based searches into a unified interface.
- Incorporation of curated biological knowledge, including catalytic site definitions and ligand-guided motifs.
- Development of a new Chemical Search tool with an integrated drawing tool and standard identifiers.
Main Results:
- A redesigned Advanced Search interface supporting intuitive 3D structure discovery.
- A new Chemical Search tool enabling definition of chemical queries within spatial and chemical contexts.
- Reduced need for detailed knowledge of residue numbering or external cheminformatics software.
Conclusions:
- The redesigned RCSB.org search interfaces enable efficient exploration of structures and chemical diversity.
- These tools support the investigation of structure-function relationships across all life domains.
- The enhanced search capabilities cater to a broad and diverse scientific community.
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