PDBj Mine is a web interface to search the PDB.

PDBj Mine has the following basic features:

1. PDBj Mine is based on a relational database.
2. Allows enhanced keyword search.
3. 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).

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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 ! phosphate

or

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

For a description of these fields, please see the brief_summary table description. Then, to search for a number of uniprot IDs:

@db_uniprot P0CS93 | Q01745

To limit this further to a specific author, use:

@db_uniprot P0CS93 | Q01745 @deposit_author Ito

It is also possible to use search operators for multiple fields, like:

@db_uniprot P0CS93 | Q01745 @deposit_author Ito | Rogers

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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

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[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.