Introduction

The RCSB.org website provides all users various options to freely search, view, analyze, and compare experimental structures (from the Protein Data Bank or PDB) and computer structure models (CSMs). In order to explore the shapes and interactions in these structures, the first order of business is to identify one or a group of structures related to a topic of interest. To include CSMs available from RCSB.org in all simple and composite searches, turn of the toggle switch so that it is cyan colored.

Search and Browse Options (Infographic)

Click on the image to access the full infographic ...

Some Definitions

Search

Specific information about the molecule(s) of interest can be used to query the 3D structure archive (including experimental structures and CSMs). Basic and advanced search options are available to search 3D structures available from RCSB.org.

• Basic Search can be run from any page on the RCSB PDB Website by simply typing a search term or a protein/DNA/RNA sequence into the Search Bar at the top of the page.
• Advanced Search can be run by clicking on the "Advanced Search" link below the Search Bar, or by using the "Advanced Search Query Builder" tool available on the top of the Search Results page.

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.

Query Results

Once a search query has been executed using either Basic Search, Advanced Search Query Builder, or the Browse options, 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 the RCSB PDB site contain links to launch searches. For example, from the Structure Summary page, each listed author contains a link to the search page. Clicking that link will run a search for all structures for which that author is listed 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.