The antigenic index: a novel algorithm for predicting antigenic determinants
Division of Biology, 147–75, California Institute of Technology Pasadena, CA 91125, USA
1Max von Pettenkofer Institute Pettenkoferstr. 9a, D-8000 Munich 2, FRG
In this paper, we introduce a computer algorithm which can be used to predict the topological features of a protein directly from its primary amino acid sequence. The computer program generates values for surface accessibility parameters and combines these values with those obtained for regional backbone flexibility and predicted secondary structure. The output of this algorithm, the antigenic index, is used to create a linear surface contour profile of the protein. Because most, if not all, antigenic sites are located within surface exposed regions of a protein, the program offers a reliable means of predicting potential antigenic determinants. We have tested the ability of this program to generate accurate surface contour profiles and predict antigenic sites from the linear amino acid sequences of well-characterized proteins and found a strong correlation between the predictions of the antigenic index and known structural and biological data.
Received on August 17, 1987; accepted on December 31, 1987
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|
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|
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|
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|
|
|
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|
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|
|
|
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|
|
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