Answers for Sample Final Problems

a. The Chou-Fasman method is based on the propensity of different amino acids to form different types of secondary structure. It then looks for patterns of these different types of residues to determine the presence of helices and strands etc. These propensity values reflect the physics of the individual amino acids ie prolines are likely to break helices because of its sidechain. b. The GOR method is based on the idea that neighboring amino acids influence the likelihood that a particular residue will adopt a particular secondary structure. It computes something like an information content by comparing the logodds ratio of probability that an amino is in a particular structure s to the probability that it is not. c. JPRED is a consensus method because it uses 6 different methods for prediction and compares/combines the results of all of them. Ultimately, it is the most accurate because if a particular secondary structure pattern is predicted using a variety of different methods then it is likely real rather than an artifact of a particular method.