DOMPLOT: A program to generate schematic diagrams of the structural domain organization within proteins, annotated by ligand contacts

Abstract

A program is described for automatically generating schematic linear representations of protein chains in terms of their structural domains. The program requires the coordinates of the chain, the domain assignment, PROSITE information and a file listing all intermolecular interactions in the protein structure. The output is a PostScript file in which each protein is represented by a set of linked boxes, each box corresponding to all or part of a structural domain. PROSITE motifs and residues involved in ligand interactions are highlighted. The diagrams allow immediate visualization of the domain arrangement within a protein chain, and by providing information on sequence motifs, and metal ion, ligand and DNA binding at the domain level, the program facilitates detection of remote evolutionary relationships between proteins.