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 :
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: