The PDB Manager is a modul to stay up-to-date with the Brookhaven Protein Data Bank (PDB). At the moment PDB grows about by 100 solved protein structures every week. In addition, existing files are modified or become obsolete. The PDB Manager is a system which analyzes the local PDB installation, downloads the missing files, and backups files that have been modified or have become obsolete.

Accession of PDB files within the PDB Manager includes their quick finding according to selected search criteria, the schematic display of the protein's sequence and structural features, and the presentation of the PDB file information on-the-fly. For quick searches against libraries of protein structures, the PDB Manager provides up-to-date PDB subset libraries which are clustered with various threshold sequence identities. Furthermore, it allows the direct submission of selected protein chains, domains or customized regions to the Structure Viewer or to the implemented search algorithms.

fig. 1

Schematic display of PDB files in the Graphical View window. The PDB Manager shows the domain information of protein chains according to the selected classification scheme (here, SCOP), active sites, disulfide bonds, modified residues and Prosite patterns.

fig. 2

PDB Info window displaying the PDB file information.