Build complex queries with Advanced Search


Click on the magnifying glass icon from the top menu bar to access Advanced Search.
Click on the magnifying glass icon from the top menu bar to access Advanced Search.

Advanced Search provides the capability of combining multiple searches of specific types of data in a logical AND or OR. The result is a list of structures that comply with ALL or ANY of the search criteria, respectively.

Individual data items are organized by category; contextual help and examples are available by selecting  . New options include quick searches by experimental and/or molecule type, searches based on structure determination method, and the ability to find structures containing interresidue connectivity (LINK records) that cannot be inferred from the primary structure.

Currently, users can build searches based on:

  • Quick Search: retrieve all PDB entries or a subset based on experimental method or molecule type
  • ID(s) and Keywords: PDB, PubMed, UniProtKB, Pfam IDs; text and keyword searching
  • Structure Annotation: structure title, description; and macromolecule name
  • Deposition: author name; deposit, release, and revision date; latest released and modified structures; Structural Genomics Project
  • Structure Features: macromolecule type; number of chains (asymmetric unit or biological assembly), entities, models, and disulfide bonds; interresidue connectivity (LINK records); molecular weight; secondary structure content; secondary structure length; SCOP, CATH, taxonomy
  • Sequence Features: sequence; translated nucleotide sequence; sequence motif; chain length; genome location
  • Chemical Components: name; ID; InChi descriptor; SMILES/SMARTS; molecular weight; chemical formula; chemical component type; binding affinity; has ligands; has modified residues; sub-components
  • Biology: Source; expression organism; Enzyme Classification; biological process; cell component; molecular function; Transporter Classification
  • Methods: experimental method; X-ray resolution, R factor, diffraction source, structure determination method, reflections, cell dimensions, software, space group, crystal properties, detector; EM assembly
  • Publication: citation; MeSH terms; PubMed abstract
  • Misc: Has external links

The number of entries matching each individual query can be shown before running the full Advanced Search.  Searches can also be filtered by removing sequence similarity.

Advanced Searches can be stored in MyPDB to be run or modified at any time.

News Index