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May 12, 2025: NPS@ updated (see NEWS).

The protein secondary structure prediction consensus
Combining methods using different approaches to predict secondary structure is useful to validate the prediction. The first step is to select the secondary structure prediction methods (see below) you want to use. Then, the secondary structure consensus prediction program generates a secondary consensus. In this consensus the most present predicted conformational state is reported for each residue.
Secondary structure prediction methods available are :

• DSC
• GORIV
• MLRC
• PREDATOR
• SIMPA96
• SOPMA

Availability in NPS@
This method is available :

• from a dedicated page
• 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
The parameters available are those of the individual methods listed above.

NPS@ Secondary consensus output example
You can see:

• the color coded prediction. A sequence line is followed by each individual prediction and by the secondary consensus (Sec.Cons line)
• the sequence length
• the percentage of each secondary element for each prediction method
• a graphic to summarize the consensus prediction
• the parameters used.
• links on the individual prediction result file

References

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