Using MSDchem to search the PDB ligand dictionary

Abstract

The PDB ligand dictionary is the chemical reference database of all the small building block molecules (e.g., amino acids, nucleic acids, and bound ligands) in the Protein Data Bank (PDB) referenced by a distinct three-letter code identifier. Since PDB files have only three-dimensional coordinate data, the role of the dictionary that of a reference resource for the actual chemical properties of small molecules, shared consistently across all PDB entries. The ligand dictionary is maintained in all sites of the Worldwide Protein Data Bank (wwPDB), the Research Collaboratory for Structural Bioinformatics (RCSB) in U.S., the Macromolecular Structure Database (MSD) in Europe, and the Protein Data Bank in Japan (PDBj), and it is exchanged on a regular basis. The MSD group at the European BioInformatics Institute (EBI) extends the dictionary into the MSDchem ligand database, which utilizes chemo-informatics packages and incorporates additional curation work. MSDchem is publicly available on the Web through the MSDchem search system, the functionality of which is described in more detail in this unit.