Introduction

RCSB.org provides tools to search, view, analyze, and compare experimental and integrative structures from the Protein Data Bank (PDB) archive, as well as computed structure models (CSMs) from AlphaFold DB and ModelArchive. To explore shapes and interactions, begin by identifying one or more structures relevant to your topic. CSMs are not included in searches by default, so users must opt in by enabling the Include CSMs option.

Search

RCSB.org offers both basic and advanced search options for finding relevant 3D structures, as well as chemical search tools for identifying small molecules.

• Basic Search can be run from any page on the RCSB PDB website by typing a search term or a protein/DNA/RNA sequence into the Search Bar at the top of the page. Learn more about Basic Search
• Advanced Search can be run by clicking on the "Advanced Search" link below the Search Bar or by visiting /search/advanced
• Chemical Search can be run by clicking on the "Chemical Search" link below the Search Bar or by visiting /search/chemical

Browse

Currently groups of experimental structures are organized and classified in various ways so that users may explore them based on their specific classifications using the Browse Annotations feature. For example, you may navigate through the archive using any one of several classification hierarchies, such as SCOP or GO (Gene Ontology), EC (Enzyme classification) and more.

Search Results

Once a search query has been executed, the search results can be listed, sorted, grouped and/or further refined using the 'Refinements' panel. The Advanced Search Query Builder displayed at the top of the search results page allows users to include additional search criteria to create composite queries.

Once a single or a group of structures related to the topic of interest has been identified you can examine it carefully and/or download structure related files for exploration and analysis. Each structure in the Search Results page opens a Structure Summary page which provides detailed information about a specific experimental structure or CSM. Similarly each group of structures can be explored from its Group Summary Page to learn more about patterns, trends, and aggregated information about members of the group.

Options for querying the archive and saving search parameters are available in MyPDB.

Query by Example

Many pages on RCSB.org include links that launch searches. For example, from the Structure Summary page, each listed author links to a search for all structures where that author is credited as the audit author.

MyPDB

Searches can be saved and run later using the MyPDB feature. MyPDB also allows you to schedule weekly email notifications of newly released structures that match a given search query. See the MyPDB documentation for more details.