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BioLiP E. coli GLASS GPCR-HGmod GPCR-RD GPCR-EXP Tara-3D TM-fold DECOYS POTENTIAL RW/RWplus EvoEF HPSF THE-DB ADDRESS Alpaca-Antibody CASP7 CASP8 CASP9 CASP10 CASP11 CASP12 CASP13 CASP14

PSSpred (Protein Secondary Structure prediction) is a simple neural network training algorithm for accurate protein secondary structure prediction. It first collects multiple sequence alignments using PSI-BLAST. Amino-acid frequence and log-odds data with Henikoff weights are then used to train secondary structure, separately, based on the Rumelhart error backpropagation method. The final secondary structure prediction result is a combination of 7 neural network predictors from different profile data and parameters. The program is freely downloadable at the bottom of this page.


PSSpred on-line

Copy and paste your sequence here (<4,000 residues, in FASTA format):

Or upload the sequence from your local computer:

Email: (mandatory, where results will be sent to)

ID: (optional, your given name of the protein)


PSSpred download

  • Click PSSpred_v4.tar.bz2 to download the current version of the PSSpred package (the programs can only be run in 64 bit Linux operating system).
    • 1. unpack the PSSpred files by "tar -jxvf PSSpred_v4.tar.bz2".
    • 2. PSSpred needs following external files. If you do not have them installed in your computer, you can download from here:
      • Click nr.tar.gz to download non-redundant sequence database.
    • 3. Run PSSpred by "PSSpred.pl seq.fasta". You need to edit the $db variable in the script to point to the location of decompressed nr library. An instruction can be found at the head of the enclosed "PSSpred.pl" file.

  • Updates of PSSpred program:
    • 2018/04/05: PSSpred V4 was released. Updates include: remove external dependency on PSI-Blast, making $db the only variable that need to be editted in PSSpred.pl.
    • 2016/03/08: PSSpred V3 was released. Updates include (1). Convert non-standard amino acids to standard ones to avoid program failure; (2). change script format so that it can adopt new PSI-Blast version; (3) a bug was fixed for the PSSpred server (mismatch between old PSSpred and new PSI-Blast format). This is the last version the dependent on blast 2.6.
    • 2012/10/01: PSSpred V2 was released. Updates include (1). Dimension is extended so that PSSpred can predict secondary structure for proteins >1000 residues (up to 4000 residues); (2). A README file is added into the PSSpred package.
    • 2011/07/10: Initial release (PSSpred V1).

    Reference

  • Renxiang Yan, Dong Xu, Jianyi Yang, Sara Walker, Yang Zhang. A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction. Scientific Reports, 3: 2619 (2013). [PDF] [Support Information]

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