Predict the secondary structure of biofilm-related protein Se0862 from Synechococcus elongatus. This small protein (125 aa) has limited sequence identity to other known proteins (that'll make it challenging for most methods relying on sequence similarity). Use both predator and psipred+ to predict the structure of this sequence.

Convienently for us, the structure of Se0862 has been solved by NMR methods and is in the PDB (PDBID 6UF2). Use DSSP or stride to assign the secondary structure of this protein. Compare each prediction to the actual secondary structure using a strip diagram. Evaluate the goodness of the prediction with a simple metric along the lines of:

• +1 for each matching H or E (a correct prediction)
• -0.5 for each H predicted to be E (or vice versa) (getting the secondary structure wrong)
• -0.25 for each residue in regular secondary structure predicted to be in the coil (shortening or missing elements of secondary structure)

How good are these methods? Is one superior for this sequence? How does the quality of the answer compare to the rough time involved in the calculation?

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