Protein Engineering, Vol. 12, No. 12, 1041-1050,
December 1999
© 1999 Oxford University Press
Prediction of protein secondary structure content
Computer-Aided Drug Discovery, Pharmacia and Upjohn, Kalamazoo, MI 49007-4940 and 1 Department of Computer and Information Science, Indiana University Purdue University Indianapolis, Indianapolis,IN 46202-5132, USA
All existing algorithms for predicting the content of protein secondary structure elements have been based on the conventional amino-acid-composition, where no sequence coupling effects are taken into account. In this article, an algorithm was developed for predicting the content of protein secondary structure elements that was based on a new amino-acid-composition, in which the sequence coupling effects are explicitly included through a series of conditional probability elements. The prediction was examined by a self-consistency test and an independent dataset test. Both indicated a remarkable improvement obtained when using the current algorithm to predict the contents of 
-helix, ß-sheet, ß-bridge, 310-helix, 
-helix, H-bonded turn, bend and random coil. Examples of the improved accuracy by introducing the new amino-acid-composition, as well as its impact on the study of protein structural class and biologically function, are discussed.
Keywords: 1st-order coupled components/-helix/ß-sheet/ß-bridge/310-helix/-helix/H-bonded turn/bend, random coil
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