PDBj Mine
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:
antibody virus
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
hydrolase -phosphate
Literal search
To perform a literal search, the " operator can be used:"galactose oxidase"
Literal search
Search specific field
It is also possible to filter your query by only searching specific fields. The following fields are available for filtering:- pdbid
- struct_title
- pdbx_descriptor
- deposit_author
- citation_author
- citation_title
- citation_journal
- citation_volume
- ligand
- exptl_method
- biol_species
- host_species
- db_pubmed
- db_doi
- db_ec_number
- db_goid
- db_uniprot
- db_pfam
- db_genbank
- db_embl
- db_pir
- db_emdb
- pdb_related
- keywords
- group_id
@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
Sequence search
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.
e.g.:
KGFEPLIQFA
[Advanced Search]
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.
[SQL Search]
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.