Understanding protein biological function is a key issue in modern biology, which is largely determined by its 3D shape. Protein 3D shape, in its turn, is functionally implied by its amino acid sequence. Since the direct inspection of such 3D structures is rather expensive and time consuming, a number of software techniques have been developed in the last few years that predict a spatial model, either of the secondary or of the tertiary form, for a given target protein starting from its amino acid sequence.
This paper offers a comparison of several available automatic secondary structure prediction tools. The comparison is of the experimental kind, where two relevant sets of proteins, a non-redundant one including 100 elements, and a 180-protein set taken from the CASP 6 contest, were used as test cases. Comparisons have been based on evaluating standard quality measures, such as the Q3 and SOV.