The Top Bar Search provides simple text-based queries using keywords, PDB ID, Authors, Structural Genomics Centers, Chemical Names and ID's.
The "PDB ID or Text" search is the default search option on the site.
A 4-character PDB ID is assigned to each new structure at the time of deposition. The IDs are automatically assigned and do not have meaning. However, they serve as the unique, immutable identifier of each entry in the Protein Data Bank. As such, they are used throughout the scientific literature (e.g. in journal articles and in other databases) to refer to entries in the Protein Data Bank. Hence, if the PDB ID of an entry in the Protein Data Bank is known, it is the most direct way to retrieve it from the database.
If the search term is not a valid PDB ID, a full text search is performed instead. This search is a Lucene full text search of the content of the structure files in mmCIF format. For example, a search for actin would return all structures that have the word actin appear somewhere in the mmCIF coordinate file. In addition, unreleased entries, citations, ligands, static web pages, and CATH, SCOP, PFAM and GO classifications are also searched.
The full text search also supports operator syntax. Currently we support AND, OR and NOT search operators. We also support exact phrase syntax. By enveloping multiple terms in double quotes ("), the query will only return hits with that exact phrase. Here are some examples on how they are used:
We also support grouping terms to form more complex queries. This is done with parentheses (). For example:
We also support wildcard searching both single character (?) or multicharacter (*). For example:
Note: Wildcard searches at the beginning of a word or word phrase are NOT supported (i.e. *synthesis)
This primary author search searches the PDB database of structures. An auto-completion feature is available. If the spelling of the author's name is recognized, an auto-completion popup menu appears.
NOTE: If the auto-completion popup menu does not appear, try entering a <space> after the name
This query searches for structures using a pull-down list of Structural Genomics Center names.
This query searches for structures containing a particular small molecule (e.g. biotin), using the small molecule names found in the Chemical Component Dictionary (formerly the HET Group Dictionary).
For example, searching for Chemical Name "Adenosine" will return all PDB structures that have a chemical component with that word in the chemical component's name or a synonym.
For the "Adenosine" example, the results will include the PDB structures with "Adenosine-5'-Triphosphate" (three letter code: ATP).
A Chemical Name search for "aspartame" will return all PDB structures that contain the ligand PME (N-L-alpha-aspartyl L-phenylalanine 1-methylester) which has the chemical synonym "Aspartame".
More information about the Chemical Component Dictionary can be found here.
This query searches for structures containing a particular chemical component (e.g. ATP, HEM, ZN, MG, F), using the "3-letter" codes found in the Chemical Component Dictionary (formerly the HET Group Dictionary). More information about the Chemical Component Dictionary can be found here.
Please contact us if, after reading the Top Bar Search explanations, additional help on searching is needed.