WPDB - PC Windows-based interrogation of macromolecular structure

WPDB version 2.0 is a Microsoft-Windows-based program for browsing and interrogating native and derived structural features of biological macromolecules using data obtained from the Protein Data Bank (PDB). Major features of WPDB are a 20-fold compression of PDB files and query and analysis tools. The latter permit the geometric and sequence properties of structures to be analyzed individually or through comparative analysis. The object-oriented software design provides a high level of interaction between display windows, which facilitates information discovery. Three examples are given to illustrate the capabilities of the software, namely: location of the distribution of the most hydrophobic residues in the acid proteases; exploration of the geometric features of a 4-helix bundle motif; and examination of the effect of antibody binding by comparison of a neuraminidase with a neuraminidase-antibody complex. Additional details are available to World Wide Web (WWW) users at the URL http://www.sdsc.edu/CCMS/ Packages/wpdb.html.