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PDB entry search (PDBj Mine)

Mine Summary page

PDBj Mine is a new generic interface to search PDB entries by PDB ID and keyword etc. See also Basic Usage.

Mine search results


Advanced Search (PDBj Mine)

Mine Advanced search

In Advanced Search, you can use combination of various conditions to search PDB entries.


Large Structures

Large structures

Large Structures are large structure entries which exceed the limitations of the original PDB file format and are released as a single entry without being split into multiple entries. Since they cannot be expressed in a PDB file, they are released as single files in PDBx/mmCIF and PDBML/XML formats in a different directories of PDB archive ftp site.
ftp site:


NMR data search (BMRB)

BMRB entry page

This service provides to search in the biomolecule NMR database BMRB.


Sequence Navigator

Sequence Superposition

Sequence Navigator is a tool to look for molecules with similar sequences.


Structure Navigator

Structure Navigator Alignment

Structure Navigator is a tool to look for molecules with similar structures.


EM Navigator

EM Navigator entry page

EM Navigator is a data browser for biological 3D electron microscopy.

EM Navigator top page


Omokage Search

omokage search top

'Omokage search' is a shape similarity search service for 3D structures of macromolecules. By comparing overall shapes, and ignoring details, similar-shaped structures are searched.




wwPDB/RDF is a collection of PDB data in the Resource Description Framework (RDF) format. The RDF format is the standard format for the Semantic Web. An ontology defined in the Web Ontology Language (OWL) is also provided for the PDB/RDF, which is a straightforward translation of the PDB mmCIF Exchange Dictionary.

URL: (PDB/RDF) (chem_comp/RDF)


SeSAW Alignment

SeSAW (Sequence-Derived Structural Alignment Weights) provides functional annotations that identifies conserved sequence and structural motifs in query proteins. See also SeSAW Tutorial.



GIRAF top page

This service is currently under (active) development.

GIRAF is a similarity search service for ligand binding sites available at this site. For a given PDB ID or uploaded PDB file, GIRAF searches for known ligand binding sites in the PDB that are similar to substructures of the query.


Latest Release Search

latest top

This service provides latest released entry list, including both newly registered entries and updated entries. Each entry ID is linked to the PDBj Mine page. All the entry ID list in PDB is also available.


Status Search

status search results

Status Search provides searching service of PDB entries which are already deposited but yet released.


2012-07-11 (last edited: more than 1 year ago)2015-05-20
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