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July 30, 2024: NPS@ updated (see NEWS).

A brief introduction to SIMPA96
SIMPA96 is a nearest neighbor secondary structure prediction method. It's based on the homologue method described by Levin et al.

Availability in NPS@
This method is available :

• from a dedicated page
• in secondary structure prediction consensus
• in protein multiple sequence alignment:
  • KALIGN
  • MAFFT
  • MSUCLE
• when you work with a sequence in NPS@ if you make a consensus secondary structure prediction on it

Parameters
No parameter required.

NPS@ SIMPA96 output example
You can see:

• 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 summarize the prediction, the second contains the reliability score for each predicted state
• the parameters used
• a link to the prediction result text file

References

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