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The PSIPRED Protein Sequence Analysis Workbench

The PSIPRED Protein Sequence Analysis Workbench aggregates several UCL structure prediction methods into one location. Users can submit a protein sequence, perform the predictions of their choice and receive the results of the prediction via e-mail or the web.
For a summary of the available methods you can 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

• Input
• Sequence Filter
• MSA Options
• DISOPRED
• BioSerf
• DomPred

Choose Prediction Methods

PSIPRED v3.3 (Predict Secondary Structure) DISOPRED3 (Disorder Prediction) pGenTHREADER (Profile Based Fold Recognition) MEMSAT3 & MEMSAT-SVM (Membrane Helix Prediction)   BioSerf v2.0 (Automated Homology Modelling) DomPred (Protein Domain Prediction) FFPred 3 (Eukaryotic Function Prediction) GenTHREADER (Rapid Fold Recognition) MEMPACK (SVM Prediction of TM Topology and Helix Packing) pDomTHREADER (Fold Domain Recognition) DomSerf v2.0 (Automated Domain Modelling by Homology) Help...

Input Sequence (Single sequence or Multiple Sequence alignments; as raw sequence or fasta format)

Help... If you wish to test these services follow this link to retrieve a test fasta sequence.

Submission Details

Email Address for job completion alert (optional) Help... Password (only required for licenced commercial e-mail addresses) Help... Short identifier for submission Help...

PFilt Options

Select Sequence masking options

Mask low complexity regions Mask transmembrane helices Mask coiled-coil regions Help... Warning: No sequence filters are applied when running MEMSAT or MEMPACK

Homologue Detection

It looks like your input may be a multiple sequence alignment; Multiple alignment input is only available for PSIPRED, pGenTHREADER and pDomTHREADER Find new close and distant relatives. Your input alignment contains only some of the possible homologues (most accurate calculation) Find new distant relatives. You are sure your input alignment contains all known close homologues Find no relatives. You are sure your input alignment contains all known homologues (likely to be least accurate) Help... Warning: These options only apply to multiple alignment input.

Prediction Options
Include PSIPRED secondary structure prediction
DISOPRED2's False Positive Threshold:	5%
Note: the threshold in False Positive Rate for DISOPRED2 predicitions is now fixed to 5%, which is the default value used by DISOPRED3.
Output Options
Don't return PSI-BLAST output Return PSI-BLAST hits only Return PSI-BLAST hits and alignments

Modeller Key:

Input your MODELLER key obtained from the Sali lab

Help...

Sequence alignment domain prediction: PSI-BLAST options
Perform PSI-BLAST based prediction:	Yes
Select database:	PfamA
PSI-BLAST e-value cutoff:
Number of PSI-BLAST iterations:
Help...
DomSSEA domain prediction options
Perform DomSSEA prediction:	Yes
Help...
PSIPRED options
Include secondary structure profile plot:	Yes No
Display PSIPRED prediction:	Yes No
Help...