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April 24th, 2024: NPS@ updated (see NEWS).

A brief introduction to PREDATOR
PREDATOR is a secondary structure prediction method based on recognition of potentially hydrogen-bonded residues in a single amino acid sequence (original server).

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
The user can choose between two database files stride.dat and dssp.dat. These files contain propensity tables, secondary structural assignments and thresholds for two secondary structure assignment methods from tertiary structure : STRIDE and DSSP.

NPS@ PREDATOR 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 score curve for each predicted state
• the parameters used
• a link to the prediction result text file

References

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