The PSIPRED Structure Analysis Workbench

The PSIPRED Structure Analysis Workbench aggregates three structural analysis methods into one location. Users can submit protein structures, perform the analysis of their choice and receive the results of the prediction via e-mail and the web.
For a summary of the available methods please read More...

NOTE: users who need to run our methods on a large number of proteins should consider downloading our software using the menu on the left (Server Navigation -> Software Download).

The PSIPRED Team
Current Contributors David T. Jones, Daniel Buchan, Tim Nugent, Federico Minneci & Kevin Bryson
Previous Contributors Anna Lobley, Sean Ward, Liam J. McGuffin

For queries regarding PSIPRED: psipred@cs.ucl.ac.uk


Choose Analysis Methods

MetSite (Protein-metal ion contact prediction) HSPred (Protein-protein hotspot residue prediction)
MEMEMBED (Membrane protein orientation predictor) Generate TDB (Generated custom threading database entries)
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Upload PDB file



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If you wish to Metsite or HSPred follow this link to retrieve a test pdb file.

Submission Details

Email Address for job completion alert (optional)

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Password (only required for licenced commercial e-mail addresses)

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Short identifier for submission

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Select Metal Site Classifier



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Prediction Chain

Indicate for which chain in the PDB file you wish to make metal binding predictions

Chain ID:
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Select False Positive Rate


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HSPred Options

Interface Definition

List chain identifiers for the proteins on either face of the interface to be analysed. Use capital letters, space separate entries (e.g. "A B").

Protein 1:

Protein 2:

If using the test pdb file linked above: input "A" for 'Protein 1' and input "B" for 'Protein 2'.
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Memembed Options

Search Type
Target is a Beta Barrel Yes No
N Terminal Location Cytoplasmic Extra cellular
Helix Boundaries (comma separated list)

Ensure you enter your valid MODELLER key via the BioSerf tab.

You input looks like it may be a multiple sequence alignment, please ensure it is in valid fasta format and that all sequences are the same length

You have selected every analysis. The run time will typically be around 5 to 6 hours. You may wish to select fewer specific analyses

Metsite will only analyse one chain in the PDB file at a time

There must be at least 2 chains in your PDB file.

MakeTDB will only analyse single chain PDB files.

Memembed will only process membrane proteins.