High throughput processing of the structural information in the protein data bank

The protein data bank (PDB) is the largest, most comprehensive, freely available depository of protein structural information, containing more than 37,500 deposited structures. On one hand, the form and the organization of the PDB seems to be perfectly adequate for gathering information from specific protein structures, by using the bibliographic references and the informative remark fields. On the other hand, however, it seems to be impossible to automatically review remark fields and journal references for processing hundreds or thousands of PDB files. We present here a family of combinatorial algorithms to solve some of these problems. Our algorithms are capable to automatically analyze PDB structural information, identify missing atoms, repair chain ID information, and most importantly, the algorithms are capable of identifying ligands with their respective binding sites.