NPS@ help : Help on SOPM tool

SOPM help

A brief introduction to SOPM
SOPM (Self-Optimized Prediction Method) is a secondary structure prediction method based on the homologue method described by Levin et al.. A new set of parameters have been optimized on a non-redundant databank of 510 sequences derived from Hobohm and Sander (PDB select 25% August 1999).
The computing time has been divided by 3.
NPS@ is the original server for this method.

Availability in NPS@
This method is available :

At URL : https://npsa-prabi.ibcp.fr/NPSA/npsa_sopm.html.

In secondary consensus prediction at URL : https://npsa-prabi.ibcp.fr/NPSA/npsa_seccons.html.

In protein sequences multiple alignement at URLs :

CLUSTALW : https://npsa-prabi.ibcp.fr/NPSA/npsa_clustalw.html

MULTALIN : https://npsa-prabi.ibcp.fr/NPSA/npsa_multalin.html

when you work with a sequence in NPS@ if you make a consensus secondary prediction on it.

Parameters
You can set the number of conformational states to predict : 3 or 4.
The similarity threshold parameter is the threshold below which a subject peptide is rejected when it's compared with a query peptide of the sequence.
The window size parameter sets the length of the peptides to use.

NPS@ SOPM output example
You can see:

MPSA/ANTHEPROT link to view the prediction in these local protein sequence analysis softwares.

The color coded prediction (a sequence line and below the corresponding predicted states).

The sequence length.

The percentage of each secondary element.

Two graphics. The first to better visualize the prediction. In the second, there are the score curves for each predicted state.

The paramaters used.

Links on the prediction result text file and on intermediate result text file.

References