Building a structured PDB: the RS-PDB database.

A method for automatically analyzing structures deposited in the Protein Data Bank is presented. The method is capable to detect missing atoms, bond length deviations, atom bumps and to correctly identify protein-ligand complexes. The results are organized into a database, called the Rich Structure PDB (RS-PDB in short) from which one can easily select PDB entries satisfying diverse sets of requirements. The newer and richer mmCIF format of both the PDB and its chemical component dictionary (formerly the HET Group Dictionary) were used in the construction, and the International Chemical Identifier (InChI) of IUPAC played a main role in correctly identifying distinct ligands.