PDBj Mine

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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.

[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 ! phosphate
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

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.



[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.

Created: 2018-02-28 (last edited: more than 1 year ago)2018-10-23
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PDB entries from 2021-06-09