Generalized ensemble methods for de novo structure prediction

Current methods for predicting protein structure depend on two interrelated components: (i) an energy function that should have a low value near the correct structure and (ii) a method for searching through different conformations of the polypeptide chain. Identification of the most efficient search methods is essential if we are to be able to apply such methods broadly and with confidence. In addition, efficient search methods provide a rigorous test of existing energy functions, which are generally knowledge-based and contain different terms added together with arbitrary weights. Here, we test different search methods with one of the most accurate and predictive energy functions, namely Rosetta the knowledge-based force-field from Baker's group [Simons K, Kooperberg C, Huang E, Baker D (1997) J Mol Biol 268: 209-225]. We use an implementation of a generalized ensemble search method to scale relevant parts of the energy function. This method, known as Hamiltonian Replica Exchange Monte Carlo, outperforms the original Monte Carlo Simulated Annealing used in the Rosetta package in terms of sampling low-energy states. It also outperforms another widely used generalized ensemble search method known as Temperature Replica Exchange Monte Carlo. Our results reveal clear deficiencies in the low-resolution Rosetta energy function in that the lowest energy structures are not necessarily the most native-like. By using a set of nonnative low-energy structures found by our extensive sampling, we discovered that the long-range and short-range backbone hydrogen-bonding energy terms of the Rosetta energy discriminate between the nonnative and native-like structures significantly better than the low-resolution score used in Rosetta.