title: OPTIMIZATION BIAS IN ENERGY-BASED STRUCTURE PREDICTION.
abstract: Physics-based computational approaches to predicting the structure of macromolecules such as proteins are gaining increased use, but there are remaining challenges. In the current work, it is demonstrated that in energy-based prediction methods, the degree of optimization of the sampled structures can influence the prediction results. In particular, discrepancies in the degree of local sampling can bias the predictions in favor of the oversampled structures by shifting the local probability distributions of the minimum sampled energies. In simple systems, it is shown that the magnitude of the errors can be calculated from the energy surface, and for certain model systems, derived analytically. Further, it is shown that for energy wells whose forms differ only by a randomly assigned energy shift, the optimal accuracy of prediction is achieved when the sampling around each structure is equal. Energy correction terms can be used in cases of unequal sampling to reproduce the total probabilities that would occur under equal sampling, but optimal corrections only partially restore the prediction accuracy lost to unequal sampling. For multiwell systems, the determination of the correction terms is a multibody problem; it is shown that the involved cross-correlation multiple integrals can be reduced to simpler integrals. The possible implications of the current analysis for macromolecular structure prediction are discussed.
authors.affiliation: Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Petrella
keywords: Energy function; conformational search; energy correction; macromolecules; optimization bias; parent distribution; probability distribution function; sampling; structure prediction