Overview: Search and Browse
The value of Protein Data Bank lies in the ability find one or groups of structures related to a topic of interest for visualization and analysis. RCSB PDB offers many ways to search, browse, and explore the archive.
- Search: When some specific information about the structure(s) of interest is known, it can be used to query the PDB archive. Various types of search options are available to explore the archive.
- A Basic Search can be run from any page on the RCSB PDB Website by simply typing a search term into the Search Bar at the top of the page.
- An 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 on the Search Results page.
- Browse: To explore groups of PDB structures organized in various ways once the archive can also be explored using the Browse Annotations feature. This allows you to search for structures by navigating through or searching in any one of several classification hierarchies, such as SCOP or GO (Gene Ontology).
Once a search query has been executed using either Basic Search, Advanced Search Query Builder, or the Browse options, the search results can be sorted, paged and further refined using the 'Refinements' panel. The search results can be rendered using several different views: "List", "Gallery", "PDB IDs", or "Tabular Reports". From the Search Results page, a Basic Search can be opened in the Advanced Search Query Builder, allowing additional search criteria to be added.
Once a structure 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 PDB structure.
Additional options for querying the archive and saving search parameters are available.
- 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 release structures that match a given search query. See the MyPDB documentation for more details.