In Advanced Search, you can use combination of various conditions to search PDB entries.
Chemie search searches non-protein and non-nucleotide compounds. Using this service, you can also find PDB entries which include the compounds.
This service provides to search in the biomolecule NMR database BMRB.
'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.
See Yorodumi Docs for more details.
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.
SeSAW (Sequence-Derived Structural Alignment Weights) provides functional annotations that identifies conserved sequence and structural motifs in query proteins. See also SeSAW Tutorial.
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.
Status Search provides searching service of PDB entries which are already deposited but yet released.