PDBj Mine is a web interface to search the PDB.
PDBj Mine has the following basic features:
- PDBj Mine is based on a relational database.
- Allows enhanced keyword search.
- Detailed queries can be performed using using SQL.
- PDBj Mine:SQL Queries provides some examples for SQL queries that can be used in PDBj Mine.
- PDBj Mine:REST API RESTful Web Service interface for PDBj Mine.
- PDBj Mine:Local Install How to locally install PDBj Mine's relational database.
- Cite us How to cite PDBj Mine
[The basics]Using the search box at the top of the PDBj web page, various components of the PDBj website can be searched, as described on the omni-search help page. A basic search performs a keyword-based search through the PDB (PDBj Mine), PDBj web-pages (e.g. help), unreleased entries (status search), Chemie (PDBj Mine) and PRD/BIRD (PDBj Mine).
Keyword search syntax
You can use special operators for keyword search: &, |, and !. The operators have the usual precedence: NOTANDOR.
AND (&) search
If multiple keywords split by & or white space are input, you will get a PDB entry list including all the keywords.
e.g.: Searching entries included both "antibody" and "virus"
antibody & virus
You can also use the following form:
OR (|) search
If multiple keywords split by | are input, you will get a PDB entry list including either keyword.
e.g.: Searching for entries including either "erythrocyte" and "leukocyte"
erythrocyte | leukocyte
Negation NOT (!)
If you want to search by excluding some keywords, add the ! or - operator before such keywords.
e.g.: Searching entries including the "hydrolase" keyword but not including the "phosphate" keyword.
hydrolase ! phosphateor
Literal searchTo perform a literal search, the " operator can be used:
Search specific fieldIt is also possible to filter your query by only searching specific fields. The following fields are available for filtering:
@db_uniprot P0CS93 | Q01745To limit this further to a specific author, use:
@db_uniprot P0CS93 | Q01745 @deposit_author ItoIt is also possible to use search operators for multiple fields, like:
@db_uniprot P0CS93 | Q01745 @deposit_author Ito | Rogers
You can also search entries including an amino acid sequence or a nucleic acid sequence. The sequence has to be in one letter form. Sequences longer than five residues can be searched.
If you want to find entries that satisfy certain conditions such as resolution, polymer types, annotations, etc., you can use the Advanced Search interface where you can specify a variety of conditions.
If the Advanced Search does not suffice your needs, you can alternatively use our SQL Search service where you can write custom, fine-grained queries in SQL, the standard query language for relational databases. To use our SQL Search, you must be familiar with SQL as well as the structure of the PDBx/mmCIF format. The structure of the relational database underlying PDBj Mine is based on that of PDBML. The categories defined in the PDBx/mmCIF dictionary are defined as tables with the data-items as columns.
For your convenience, the brief_summary table and some helper functions are defined. The brief_summary table compiles the information used by our Advanced Search. A detailed description of the structure of our relational database is given on the PDBj Mine 2 RDB documentation page
Several examples of SQL queries are presented in PDBj Mine:SQL Queries.