Ab initio prediction Ab initio = from the beginning"; in strictest sense uses first principles, not information about other protein structures In practice all methods rely on empirical observations about other structures Force fields Knowledge-based scoring functions Training sets Fragment structures a good review: Bonneau, R, and D Baker. "Ab Initio Protein Structure Prediction: Progress and Prospects. "Rev Biophys Biomol Struct 30(2001):17389Ab initio prediction • Ab initio = “from the beginning”; in strictest sense uses first principles, not information about other protein structures • In practice, all methods rely on empirical observations about other structures – Force fields – Knowledge-based scoring functions – Training sets – Fragment structures A good review: Bonneau, R, and D Baker. "Ab Initio Protein Structure Prediction: Progress and Prospects." Rev Biophys Biomol Struct. 30 (2001): 173-89