Anders Krogh, Soren Riis
Most current methods for prediction of protein secondary structure use a small window of the protein sequence to predict the structure of the central amino acid. We describe a new method for prediction of the non-local structure called ,8-sheet, which consists of two or more ,8-strands that are connected by hydrogen bonds. Since,8- strands are often widely separated in the protein chain, a network with two windows is introduced. After training on a set of proteins the network predicts the sheets well, but there are many false pos(cid:173) itives. By using a global energy function the ,8-sheet prediction is combined with a local prediction of the three secondary structures a-helix, ,8-strand and coil. The energy function is minimized using simulated annealing to give a final prediction.