Welcome to the PDB2RDF project website

The Protein Data Bank (PDB) is a global repository for biomolecular structure such as proteins nucleic acis, molecular complexes, viruses and complete ribosome assemblies as determined through solid state and solution NMR spectroscopy, cryo-electron microscopy and X-Ray crystallography.

PDB2RDF, an RDFizer for the XML representation of PDB (PDBML) that aims to provide a referenceable knowledge representation scheme for every entity contained within PDB, whether it be structural (molecules, atoms, bonds), experimental (details of the structural determination experiments) or elements of provenance (deposition details such as dates or literature references).

The Linked Data generated by PDB2RDF is accessible through a Virtuoso OpenLink powered triplestore. We have also developed a PDB2RDF viewer that operates by inderectly posting asynchronous SPARQL queries to the triple store through a proxy. Molecular structures can be visualized using an in-house version of Jmol which directly consumes PDB2RDF's RDF.

This project has been also made available through our Google Code project website.