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Article Dans Une Revue Protein Engineering Année : 1997

Exploring the limits of nearest neighbour secondary structure prediction

Résumé

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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Dates et versions

hal-02698585 , version 1 (01-06-2020)

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Citer

Jonathan Levin. Exploring the limits of nearest neighbour secondary structure prediction. Protein Engineering, 1997, 10 (7), pp.771-776. ⟨10.1093/protein/10.7.771⟩. ⟨hal-02698585⟩

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