The STR alphabet

The STR (Strand) alphabet is an enhanced version of DSSP currently being developed at University of California, Santa Cruz. The concept was originated by post-doc Yael Mandel-Gutfreund. We have found that two-track hidden Markov models built with a STR secondary track are particularly good at fold recognition and target-template alignments.

The original DSSP alphabet uses the letters "H" (alpha helix), "B" (isolated beta-bridge), "E" (extended strand in beta ladder), "G" (3/10 helix), "I" (pi helix), "T" (H-bonded turn) and "S" (bend).

STR subdivides DSSP letter "E" into 6 letters, according to properties of a residue's relationship to its strand partners. (We also group the rare pi helix class "I" with the alpha helix class "H".)

In the diagram above, dots indicate the strand of the residue being assigned. In a beta sheet, this strand is either surrounded by two parallel partners "P", two anti-parallel partners "A" or one anti-parallel and one parallel partner "M". Edge strands (that have only one beta strand partner) have either a parallel partner "Q" or an anti-parallel partner "Z". Finally, we retain the "E" label for strand residues to which DSSP assigns no partners (generally beta bulges).

We have also defined STR2 and STR3 alphabets:

The STR2 alphabet further divides the anti-parallel edge strand class (Z) into two classes---those residues that are hydrogen-bonded to the sheet (Y) and those that are not (Z).

The STR3 alphabet has Y and Z as in STR2, but also splits the parallel edge strand class into Q and R. (Question: which is the hydrogen-bonded one?)