PDBtool: An interactive browser and geometry checker for protein structures

PDBtool version 1.0 is an interactive UNIX and X/Motif-based computer program for investigating the three-dimensional (3D) structure of proteins using data represented by the Protein Data Bank (PDB) format. Major components of PDBtool include a three-dimensional structure viewer, text browsers from which to investigate components of the structure under study and a comprehensive set of geometry-checking tools. The object-oriented software design provides a high level of interaction between display windows in an effort to provide a more intuitive level of interaction than is possible with existing tools. Examples of the use of PDBtool are provided to illustrate these capabilities. These include: analyzing the distribution of cysteines in a member of the family of short-chain neurotoxins; for the same protein, analyzing outliers in a Ramachandran plot and their associated isotropic temperature factors; and investigating the distribution of heme groups in human deoxyhemoglobin. A detailed description of PDBtool, including a tutorial, is available on the World Wide Web at the URL http:// www.sdsc.edu/CCMS/Packages/PDBtool.html.