Protein structural topology: Automated analysis and diagrammatic representation

The topology of a protein structure is a highly simplified description of its fold including only the sequence of secondary structure elements, and their relative spatial positions and approximate orientations. This information can be embodied in a two-dimensional diagram of protein topology, called...

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Bibliographic Details
Published in:Protein science 1999-04, Vol.8 (4), p.897-904
Main Authors: WESTHEAD, DAVID R., SLIDEL, TIMOTHY W.F., FLORES, TOMAS P.J., THORNTON, JANET M.
Format: Article
Language:English
Subjects:
Algorithms
Chemistry, Physical - methods
Computer Simulation
Models, Chemical
Models, Molecular
Protein Conformation
protein structure
Software
topological diagram
topological representation
topology
TOPS
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Summary:The topology of a protein structure is a highly simplified description of its fold including only the sequence of secondary structure elements, and their relative spatial positions and approximate orientations. This information can be embodied in a two-dimensional diagram of protein topology, called a TOPS cartoon. These cartoons are useful for the understanding of particular folds and making comparisons between folds. Here we describe a new algorithm for the production of TOPS cartoons, which is more robust than those previously available, and has a much higher success rate. This algorithm has been used to produce a database of protein topology cartoons that covers most of the data bank of known protein structures.
ISSN:0961-8368
1469-896X
DOI:10.1110/ps.8.4.897