PROTEUS
Proteus is a secondary structure prediction method that performs structure-based sequence alignments as part of the secondary structure prediction process. Integrating structural alignment with sequence-based secondary structure methods and generating a consensus result, this new method achieves an average Q3 score of 81.3% and can achieve a Q3 score approaching 88%. As a reference point, PSIPRED 2.0 is capable of achieving an average Q3 score of nearly 78%.
If you use Proteus please cite: S. Montgomerie, S. Sundararaj, W. J. Gallin, and D. S. Wishart (2006) "Improving the accuracy of protein secondary structure prediction using structural alignment" BMC Bioinformatics 7:301. doi:10.1186/1471-2105-7-301.
Manual: http://wks16338.biology.ualberta.ca/proteus/documentation.jsp#how
INPUT = Protein Sequences