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Protein Eng. 1997 Jul;10(7):771-6.

Exploring the limits of nearest neighbour secondary structure prediction.

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  • 1Unité de Bioinformatique, Bat. de Biotechnologie, INRA, Jouy-en-Josas, France.


This paper presents a simple and robust secondary structure prediction scheme (SIMPA96) based on an updated version of the nearest neighbour method. Using a larger database of known structures, the Blosum 62 substitution matrix and a regularization algorithm, the three state prediction accuracy is increased by 4.7 percentage points to 67.7% for a single sequence and up to 72.8% when using multiple alignments. The increase in prediction accuracy with respect to the previous version can be almost entirely ascribed to the sevenfold increase in the size of the database. A more detailed analysis of the results shows that badly predicted regions of a protein sequence are randomly distributed throughout the database and that the goal of perfect secondary structure predictions by methods which use only local sequence information is illusory.

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