PSIPRED - protein secondary structure prediction


PSIPRED - Accurate protein secondary structure prediction

psipred is a simple and accurate secondary structure prediction method, incorporating two feed-forward neural networks which perform an analysis on output obtained from PSI-BLAST (Position Specific Iterated - BLAST). Using a very stringent cross validation method to evaluate the method's performance, PSIPRED 3.2 achieves an average Q3 score of 81.6%.

Input Files

  • Fasta Text : Paste a text of sequencs in Fasta format
    OR
  • Fasta File : Path to Sequences in Fasta Format

Input Parameters

  • dbName : Chooses between 'swissprot','nr','pdb' for blast.

  • No Of Filter Iteration : This controls the amount of "smoothing" that is carried out on the final prediction. The recommended setting is 1, but it may be worth trying higher values to increase the level of smoothing.

  • helixBias : These options control the bias for helix and strand predictions.The default values are equal to 1.0, but if you know your protein is, for example, mostly comprised of helices then you can increase the bias towards Helix prediction.

  • strandBias : These options control the bias for helix and strand predictions.The default values are equal to 1.0, but if you know your protein is, for example, mostly comprised of beta strands then you can increase the bias towards beta strand prediction.

Displayed Results

Results have 2 tabs

  • Horizontal Format : For each amino acid a secondary structure prediction is given along with a confidence score.
    Keys for horizontal format:
    Conf: Confidence (0=low, 9=high)
    Pred: Predicted secondary structure color coded AA: Target sequence

  • Vertical Format :The above information in table format.

Downloadable Results

  • Results : psipred horizontal format. For each amino acid a secondary structure prediction is given along with a confidence score.
    Keys for horizontal format:
    Conf: Confidence (0=low, 9=high)
    Pred: Predicted secondary structure (H=helix, E=strand, C=coil)
    AA: Target sequence

  • Vertical Format : psipred vertical format

  • Log FIle : Execution log.

PSIPRED - Reference

http://bioinf.cs.ucl.ac.uk/psipred/

Contact

Prof. R. Sowdhamini(mini@ncbs.res.in)
Oommen K. Mathew (oommenkm@ncbs.res.in)
Murugavel P