UNIT 14.3 Using MSDchem to Search the PDB Ligand Dictionary

  1. Dimitris Dimitropoulos,
  2. John Ionides,
  3. Kim Henrick

Published Online: 1 OCT 2006

DOI: 10.1002/0471250953.bi1403s15

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Dimitropoulos, D., Ionides, J. and Henrick, K. 2006. Using MSDchem to Search the PDB Ligand Dictionary. Current Protocols in Bioinformatics. 15:14.3:14.3.1–14.3.21.

Author Information

  1. European Bioinformatics Institute, Hinxton, Cambridgeshire, United Kingdom

Publication History

  1. Published Online: 1 OCT 2006
  2. Published Print: SEP 2006


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.


  • ligands;
  • organic chemicals;
  • chemical structure;
  • chemical properties;
  • protein structure databases;
  • macromolecular complexes;
  • amino acids;
  • nucleic acids