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Bioinformatics Advance Access published online on July 26, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti595
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received June 2, 2005
Revised July 21, 2005
Accepted July 21, 2005

Article

CHORAL: a differential geometry approach to the prediction of the cores of protein structures

Rinaldo W. Montalvão 1*, Richard E. Smith 1, Simon C. Lovell 2, and Tom L. Blundell 1

1 Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
2 Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK; Present address: Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK

* To whom correspondence should be addressed.
Rinaldo W. Montalvão, E-mail: rinaldo{at}cryst.bioc.cam.ac.uk


  Abstract

Motivation: Although the cores of homologous proteins are relatively well conserved, amino acid substitutions lead to significant differences in structures of divergent superfamilies. Thus, the classification of amino acid sequence patterns and the selection of appropriate fragments of the protein cores of homologues of known structure are important for accurate comparative modelling.

Results: CHORAL utilizes a knowledge-based method comprised of an amalgam of differential geometry and pattern recognition algorithms to identify conserved structural patterns in homologous protein families. Propensity tables are used to classify and to select patterns that most likely represent the structure of the core for a target protein. In our benchmark CHORAL demonstrates a performance equivalent to that of MODELLER.

Availability: The algorithm is available via internet on http://www-cryst.bioc.cam.ac.uk/servers.html.


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