Protein structural topology: Automated analysis and diagrammatic representation

The topology of a protein structure is a highly simplified description of i ts fold including only the sequence of secondary structure elements, and th eir relative spatial positions and approximate orientations. This informati on can be embodied in a two-dimensional diagram of protein topology, called a TOPS cartoon. These cartoons are useful for the understanding of particu lar folds and making comparisons between folds. Here we describe a new algo rithm for the production of TOPS cartoons, which is more robust than those previously available, and has a much higher success rate. This algorithm ha s been used to produce a database of protein topology cartoons that covers most of the data bank of known protein structures.