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Protein Engineering, Vol. 14, No. 4, 227-231, April 2001
© 2001 Oxford University Press

An approach to improving multiple alignments of protein sequences using predicted secondary structure

Andrew J. Jennings1,2, Colin M. Edge1 and Michael J.E. Sternberg3

1 Discovery Chemistry, SmithKline Beecham Pharmaceuticals, New Frontiers Science Park, Third Avenue, Harlow, Essex CM19 5AW and 3 Biomolecular Modelling Laboratory, Imperial Cancer Research Fund, Lincoln's Inn Fields, P.O. Box 123, London WC2A 3PX, UK

The object of this work was to improve multiple sequence alignments using public-domain software and methods as far as possible. A method is described where the secondary structure of proteins is predicted and this information, coupled with a simplified description of the amino acids, is used to produce multiple sequence alignments. This method improved the accuracy of the resulting alignments by between 5 and 14% when compared with full sequence profile alignments (as scored against structural alignments). These improved alignments were used to predict the secondary structure of the sequences they contain. The resultant predictions were more accurate than those produced from less optimal alignments. An improvement of 6% for a three-state (helix, sheet and coil) prediction was observed when using the best alignment from the method presented here and the alignment obtained using sequence only. The method makes use of public domain software and all the associated files required to repeat the work are available from the primary author.


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