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Protein structural topology: Automated analysis and diagrammatic representation

Published online by Cambridge University Press:  01 April 1999

DAVID R. WESTHEAD
Affiliation:
The European Bioinformatics Institute, EMBL Outstation, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom Current address: School of Biochemistry and Molecular Biology, University of Leeds, Leeds, Yorkshire LS2 9JT, United Kingdom
TIMOTHY W.F. SLIDEL
Affiliation:
The European Bioinformatics Institute, EMBL Outstation, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
TOMAS P.J. FLORES
Affiliation:
Synomics Ltd., P.O. Box 71, Royston SG8 8TE, United Kingdom
JANET M. THORNTON
Affiliation:
The European Bioinformatics Institute, EMBL Outstation, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom Biomolecular Structure and Modelling Unit, Department of Biochemistry and Molecular Biology, University College, London WC1E 6BT, United Kingdom Laboratory of Molecular Biology, Department of Crystallography, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
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Abstract

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.

Type
Research Article
Copyright
© 1999 The Protein Society

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