We defined alpha/beta proteins as proteins with at least 20% of the
residues in a helix, and all beta proteins as those that have less
than 20% of the residues in a helix. There are several reasons why we
did not use 0% vesus not 0% as criterion. When using completely
automated ways to determine secondary structure (such as dssp), quite
often a few residues are labelled as being in a helix when in truth
they aren't. Even when looking at the 3D structure itself, there might
be some ambiguity whether or not certain residues form a helix. And
even if they do, if only 5 out of 150 residues are in a helix, should
this protein really be classified as alpha/beta? From previous
studies, we found the 20% cutoff to be a reasonable choice. Of course
it is debatable whether or not this choice is optimal, but the
database and scores were derived using this definition.