RCSB protein data Bank: Next-generation advanced search for exploration of experimental structures and computed structure models.

Authors

Yana Rose, Ronald Brown, Maria Voigt, Charmi Bhikadiya, Sebastian Bittrich, Jose M Duarte, Joan Segura, Rachel Kramer Green, Stephen K Burley

Published in

Protein science : a publication of the Protein Society. Volume 35. Issue 8. Pages e70731.

Abstract

The Protein Data Bank (PDB), established in 1971, is the primary global, open-access archive for experimentally determined 3D macromolecular structures (proteins, RNA, DNA). The research-focused RCSB.org web-portal provides access to these data alongside more than one million machine-learning-predicted structure models, greatly expanding the available structural landscape. Rapid growth of both experimental and computational structures has increased the need for powerful yet accessible search tools that serve a broad and diverse scientific community. Herein, we describe a redesigned RCSB Protein Data Bank RCSB.org Advanced Search capability that supports intuitive discovery of 3D structures through a unified interface. This interface integrates annotation-, sequence-, and 3D structure-based searches, embeds an interactive 3D viewer, and incorporates curated biological knowledge, such as catalytic site definitions from Mechanism and Catalytic Site Atlas and ligand-guided structural motifs, for constructing geometry-driven queries. A new Chemical Search tool allows definition of chemical queries via an integrated drawing tool or standard identifiers, seamlessly combining them with annotation filters. By allowing query definition directly within spatial and chemical contexts, these search interfaces reduce the need for detailed knowledge of residue numbering, chain identifiers, or external cheminformatics software. This capability enables efficient exploration of structures, chemical diversity, and structure-function relationships across all life domains. The redesigned interfaces can be accessed directly at rcsb.org/search/advanced for Advanced Search and rcsb.org/search/chemical for Chemical Search.

PMID:
42517697
Bibliographic data and abstract were imported from PubMed on 28 Jul 2026.

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