PROTEUS is an universal protein structure prediction server that will take any query protein sequence and predict the secondary structure, membrane spanning helices, membrane spanning beta strands, signal peptides, and 3D structures.For water-soluble protein Proteus is able to achieve a very high level of accuracy (Q3=88%, SOV=90%). In the rare situation (20-30%) where a query protein shows no similarity whatsoever to any known structure, PROTEUS is still able to achieve a Q3 score of 79%. Proteus is not restricted to generating accurate secondary structures for water-soluble proteins, as it appears to perform well for integral membrane proteins (both helix-containing proteins and beta-sheet containing porins) that have remote homologues or a portion of a homologue in the PDB.
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Scott Montgomerie, Shan Sundararaj, Warren J Gallin and David S Wishar
Improving the accuracy of protein secondary structure prediction using structural alignment
BMC Bioinformatics 2006, 7:301