PROTEUS Structure Prediction Server 2.0
Comprehensive 2D and 3D structure predictions
  Welcome to PROTEUS2

PROTEUS2 is a web server designed to support comprehensive protein structure prediction and structure-based annotation. PROTEUS2 accepts either single sequences (for directed studies) or multiple sequences (for whole proteome annotation) and predicts the secondary and, if possible, tertiary structure of the query protein(s). Unlike most other tools or servers, PROTEUS2 bundles signal peptide identification, transmembrane helix prediction, transmembrane β-strand prediction, secondary structure prediction (for soluble proteins) and homology modeling (i.e. 3D structure generation) into a single prediction pipeline. Using a combination of progressive multi-sequence alignment, structure-based mapping, hidden Markov models, multi-component neural nets and up-to-date databases of known secondary structure assignments, PROTEUS2 is able to achieve among the highest reported levels of predictive accuracy for signal peptides (Q2=94%), membrane spanning helices (Q2=87%) and secondary structure (Q3 score of 81.3% ). PROTEUS2's homology modeling services also provide high quality 3D models that compare favorably with those generated by SWISS-MODEL (within 0.2 Å RMSD). The average PROTEUS2 prediction takes ~2 minutes per query sequence. Source code is also freely available here.
If you use PROTEUS2 in your research, please cite:

Montgomerie S, Cruz JA, Shrivastava S, Arndt D, Berjanskii M, Wishart DS. PROTEUS2: a web server for comprehensive protein structure prediction and structure-based annotation. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W202-9. Epub 2008 May 15.

PROTEUS2 Queue Information = Currently 0 sequences are in queue.

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. You may also specify the source of the sequence.

Run Secondary Structure Prediction

Organism type is required only when signal peptide prediction is expected
Gram negative prokaryote Gram positive prokaryote Eukaryote

Paste Sequence (Single or multiple sequence(s) in FASTA format (example) or a single raw sequence)

OR Select a file to upload (FASTA format)



Results View results in web browser Email me when results are done
3D Structure
Run homology modelling

If you know a PDB file exists with a similar structure to your query sequence, you may upload a PDB file here, or specify a PDB accession number.
Select a PDB file
OR enter a PDB accession number

Running energy minimization can improve the accuracy of the model, but will take longer
Run energy Minimization


Video Tutorial

The PROTEUS2 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 form.
PROTEUS2 last updated July 8, 2015