Search the PDB Database

There are several ways to search the PDB. These methods can be accessed from the top frame of the site or from the left-hand navigation bar.

The results of any query is either a single structure or multiple structures that meet the search criteria. A single structure will return a Structure Summary page, multiple structures will return a Query Result Browser. Each structure is identified by a PDB ID - a 4 character code e.g., 2CPK.

PDB ID or Keyword Search From the top frame of the site

Enter a PDB identification code (PDB ID) or keyword.
Press Search

Note: This search searches the PDB database of structures and web pages on the PDB site. The results of both are returned and can be viewed individually by clicking the corresponding tab.

Searching from the left hand navigation bar

The following types of searches are available.

Top Bar Search: provides several simple text-based searches [more information]

Advanced Search:

The advanced search provides several very powerful features for querying the PDB database. We use javascript in order to support many of the dynamic and extensible features of the interface. While most popular browsers/platforms combinations are supported, we are interested in understanding any issues that may arise. Please contact us at info@rcsb.org.

Perform a simple query

To perform a simply query using the advanced interface use the menu choices on the left to pick the query type. Then choose, or enter, the appropriate parameters for the specific query. Click on “Evaluate Query” to search the PDB database.

For example:

To perform a simple Keyword search, select the “Keyword” choice in the pull-down menu.

Enter the phrase, “oncogene” in the text box and select “Evaluate Query”. The number of available structures appears to the left of the button.

Mousing over this value shows the first several PDB IDs in the result set. Clicking on this number value will navigate to the results page. The same thing would occur if you clicked on the “Evaulate Query” button.

Notice the hit count in the above image. This is a hyperlink to the subquery results.

Perform a more complicated query

To extend a simple query click on the ‘+’ button. This adds another query interface to the existing (default) interface and provides the user with an array of subqueries.

Each of these subqueries can be used to find structures of “any” or “all” by selecting the “Match pull-down menu” in the upper left corner of the window. Several searches may require control over redundancy in the result set. This can be achieved by using the removing similar sequences option before evaluating a query. Finally, to evaluate the query and navigate to the query results page, click on the "Evaluate Query" button in the lower right corner.

The following is a list of available queries:

Click here for a quick view of the available searches.

Latest Release: Displays the entries in the latest release of the PDB in the Query Results Browser.

Search Status: searches on the status of an entry, on hold or released [more information]

Search Models: searches for theoretical models that as of July 1, 2002 have been separated from the main archive .

Sequence Search: searches for short sequence patterns or for longer sequences using the program of W.R. Pearson [more information]

There are two ways to search by sequence:

1. Use the Sequence Search interface:

Click the Search tab and expand the Search Database menu item. Click on Sequence to load the sequence search interface.

There are two methods to searching the PDB database using the sequence tool.

1. Enter a PDB ID and associated chain Id.

--or--

2. Copy and past the sequence into the sequence text area.

The E cut-off value limits the number of scores and alignments shown based on the expected number of scores. A cutoff value of 2.0 will show all the library sequences with scores with an expectation value <= 2.0.

NOTE: For protein searches, library sequences with E() values < 0.01 for searches of a 10,000 entry database are almost always homologous.

There are two choices for search methods:

1. Blast Search - Sequence Search using blastp from NCBI [Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. Basic local alignment search tool. J. Mol. Biol. 215:403-410 (1990)]

2. FASTA Search - Sequence search using the program of W.R. Pearson [Pearson, W.R. and Lipman, D.J. Improved tools for biological sequence comparison. PNAS 85:2444-2448(1988)]

2. Use the advanced search tool:

Click the Search tab and expand the Search Database menu item. Select the Sequence (FLASTA/BLAST) option under the Choose a Query Type pull-down menu.

You may also use the Advanced Search quick link located on the top navigation bar ().

There are two methods to searching the PDB database using the sequence tool.

1. Use a PDB ID and associated chain.

--or--

2. copy and past the sequence into the sequence text area.

Click the Evaluate Query button to retrieve the results.

NOTE: For protein searches, library sequences with E() values < 0.01 for searches of a 10,000 entry database are almost always homologous.

There are two choices for search methods:

2. FASTA Search - Sequence search using the program of W.R. Pearson [Pearson, W.R. and Lipman, D.J. Improved tools for biological sequence comparison. PNAS 85:2444-2448(1988)]

Hints on Searching:

To find entries for a specific type of protein (for example, 'insulin') enter the protein name in the search box on the home page and then click on the Search button.
Case is ignored during a search.
A single structure is composed of components, most notably polymers, which can be analyzed individually.
You may link to the PDB Structure Summary WWW pages for specific entries directly if you know their four letter identification code(s). [more information]