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## Assessment of secondary structure prediction accuracy

The accuracy of prediction was assessed by comparison to DSSP [52]. We applied the same 8 to 3 state reduction scheme throughout. E and B were taken as strand, H as helix and all other states were taken as coil. This removes the 310-helix state from the definition, but given that the 310-helix state represents a weak 1 kcal/mol hydrogen bond, this seems reasonable, as it does not normally represent core secondary structure. Single residue -bridges (B) were included, as they do form part of core structures, however these structures are typically difficult to predict accurately. Removing single residue -bridges improves the apparent average Q3 prediction accuracy by at least 1% (data not shown).

James Cuff
2001-06-29