The protein structure prediction problem consists of determining a protein’s three-dimensional structure from the underlying sequence of amino acids. A standard approach for predicting such structures is to conduct a stochastic search of conformation space in an attempt to find a conformation that optimizes a scoring function. For one subclass of prediction protocols, called template-based modeling, a new protein is suspected to be structurally similar to other proteins with known structure. The solved related proteins may be used to guide the search of protein structure space. There are many potential applications for statistics in this area, ranging from the development of structure scores to improving search algorithms. This dissertation focuses on strategies for improving structure predictions by incorporating information about closely related “template” protein structures into searches of protein conformation space. This is accomplished by generating density estimates on conformation space via various simplifications of structure models. By concentrating a search for good structure conformations in areas that are inhabited by similar proteins, we improve the efficiency of our search and increase the chances of finding a low-energy structure. In the course of addressing this structural biology problem, we present a number of advances to the field of Bayesian nonparametric density estimation. We first develop a method for density estimation with bivariate angular data that has applications to characterizing protein backbone conformation space. We then extend this model to account for multiple angle pairs, thereby addressing the problem of modeling protein regions instead of single sequence positions. In the course of this analysis we incorporate an informative prior into our nonparametric density estimate and find that this significantly improves performance for protein loop prediction. The final piece of our structure prediction strategy is to connect side-chain locations to our torsion angle representation of the protein backbone. We accomplish this by using a Bayesian nonparametric model for dependence that can link together two or more multivariate marginals distributions. In addition to its application for our angular-linear data distribution, this dependence model can serve as an alternative to nonparametric copula methods.

Thesis (M. Sc.)--University of Alberta, 2009. / Title from pdf file main screen (viewed on Dec. 11, 2009). "A thesis submitted to the Faculty of Graduate Studies and Research in partial fulfillment of the requirements for the degree of Master of Science in Statistics, Department of Mathematical and Statistical Sciences, University of Alberta." Includes bibliographical references.

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Differential item functioning (DIF) can occur across age, gender, ethnic, and/or linguistic groups of examinee populations. Therefore, whenever there is more than one group of examinees involved in a test, a possibility of DIF exists. It is important to detect items with DIF with accurate and powerful statistical methods. While finding a proper DIP method is essential, until now most of the available methods have been dominated by applications to large scale testing contexts. Since the early 1990s, Ramsay has developed a nonparametric item response methodology and computer software, TestGraf (Ramsay, 2000). The nonparametric item response theory (IRT) method requires fewer examinees and items than other item response theory methods and was also designed to detect DIF. However, nonparametric IRT's Type I error rate for DIF detection had not been investigated. The present study investigated the Type I error rate of the nonparametric IRT DIF detection method, when applied to moderate-to-small-scale testing context wherein there were 500 or fewer examinees in a group. In addition, the Mantel-Haenszel (MH) DIF detection method was included. A three-parameter logistic item response model was used to generate data for the two population groups. Each population corresponded to a test of 40 items. Item statistics for the first 34 non-DIF items were randomly chosen from the mathematics test of the 1999 TEVISS (Third International Mathematics and Science Study) for grade eight, whereas item statistics for the last six studied items were adopted from the DIF items used in the study of Muniz, Hambleton, and Xing (2001). These six items were the focus of this study.

This thesis proposed two nonparametric statistical tests, based on the Kolmogorov-Smirnov distance and L2 mallows disatnce. To implement the proposed tests, nonparametric bootstrap method is employed to approximate the distributions of the test statistics to construct the corresponding bootstrap confidence interval procedures. Monte-Carlo simulations are performed to investigate the actual type I error of the proposed bootstrap procedures. It is found that the type I error of the bootstrap BC confidence interval procedure is close to the nominal level when censoring is not heavy and the boosttrap percentile confidence interval procedure works well when Kolmogorov-Smirnov distance is used to characterize the equivalence. When the data is heavily censored, the procedures based on the Kolmogorov-Smirnov distance have very conservative type I errors, while the procedures based on the Mallows distance are very liberal. / Thesis (Ph.D, Mathematics & Statistics) -- Queen's University, 2007-08-01 10:43:32.345

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Thesis (Ph.D.)--Baylor University, 2008. / Includes bibliographical references (p. 64-65)

Thesis (M.Sc.) - Carleton University, 2008. / Includes bibliographical references (p. 114-117). Also available in electronic format on the Internet.

Thesis (Ph. D.)--University of Missouri-Columbia, 1997. / Typescript. Vita. Includes bibliographical references (leaves 431-432). Also available on the Internet.