Proteus Structure Prediction Server
Comprehensive Secondary Structure Predictions
  Welcome to Proteus
Check out the newer version, PROTEUS2!
Proteus is a high-performing integrated web server and a stand-alone application three high-performing de novo structure prediction methods (PSIPRED, JNET and TRANSSEC [a locally developed predictor]), a jury-of-experts consensus tool and a robust PDB-based structure alignment process to generate all of its secondary structure predictions. 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. The 2D-to-3D structure mapping is accomplished with a continually updated PDB secondary structure database available for download (see the downloads section).
If you use Proteus in your research, please cite:

Montgomerie S, Sundararaj S, Gallin WJ, and Wishart DS. Improving the accuracy of protein secondary structure prediction using structural alignment. BMC Bioinformatics. 2006 Jun 14;7:301.

Submitting a sequence

You can submit your sequence in FASTA Format by pasting the sequence in the box below, or by uploading the file directly to the server.  A prediction will be returned to you.

Paste Single Sequence (FASTA format or raw sequence)

OR Select a file to upload (FASTA format, single sequence)



Results View results in web browser Email me when results are done


The Proteus web server has been verified with Mozilla Firefox, Safari, Internet Explorer 5.5 and above, and Opera 7.6 and above.
If you submit a sequence with the "View results in web browser" option checked, and the page does not refresh and show progress, your browser is likely not supported (it must support XMLHttpRequest). If this is the case, please re-submit using the "email me when results are done" option.

Problems, questions or comments? Please use our feedback page.
Last updated July 8, 2015