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.
Updates of PSSpred program:
Click PSSpred_v3.tar.gz to download
the current version of the PSSpred package (the programs can only
implemented in 64 bit Linux machines).
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).
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.
1, unpack the PSSpred files by "tar -zxvf PSSpred_v3.tar.gz".
2, Run PSSpred by "PSSpred.pl seq.fasta".
An instruction can be found at the head of the enclosed "PSSpred.pl" file.
3, PSSpred needs following external files. If you do not have
them installed in your computer, you can download from here:
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).
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