probability thresholds for helix and strand nucleations are constant but not necessarily equal; originally 1.03 was set as the helix cutoff and 1.00 for the strand cutoff. Turns are also evaluated in four-residue windows, but are calculated using a multi-step procedure because many turn regions contain amino acids that could also appear in helix or sheet regions. Four-residue turns also have their own characteristic amino acids; proline and glycine are both common in turns. A turn is predicted only if the turn probability is greater than the helix or sheet probabilities and a probability value based on the positions of particular amino acids in the turn exceeds a predetermined threshold. The turn probability p(t) is determined as: where j is the position of the amino acid in the four-residue window. If p(t) exceeds an arbitrary cutoff value (originally 7.5e–3), the mean of the p(j)'s exceeds 1, and p(t) exceeds the alpha helix and beta sheet probabilities for that window, then a turn is predicted. If the first two conditions are met but the probability of a beta sheet p(b) exceeds p(t), then a sheet is predicted instead. See also List of protein structure prediction software References External links Gerald D. Fasman on the Internet Bioinformatics Protein methods