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
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).
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1. unpack the PSSpred files by "tar -jxvf PSSpred_v4.tar.bz2".
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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]
