Browsing University of Waterloo by Subject "protein structure"
Now showing items 1-7 of 7
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Conformational Ensemble Generation via Constraint-based Rigid-body Dynamics Guided by the Elastic Network Model
(University of Waterloo, 2011-08-29)Conformational selection is the idea that proteins traverse positions on the conformational space represented by their potential energy landscape, and in particular positions considered as local energy minima. Conformational ... -
FlexSADRA: Flexible Structural Alignment using a Dimensionality Reduction Approach
(University of Waterloo, 2005)A topic of research that is frequently studied in Structural Biology is the problem of determining the degree of similarity between two protein structures. The most common solution is to perform a three dimensional ... -
Loop Modeling in Proteins Using a Database Approach with Multi-Dimensional Scaling
(University of Waterloo, 2013-09-26)Modeling loops is an often necessary step in protein structure and function determination, even with experimental X-ray and NMR data. It is well known to be difficult. Database techniques have the advantage of producing ... -
New Algorithms for Predicting Conformational Polymorphism and Inferring Direct Couplings for Side Chains of Proteins
(University of Waterloo, 2015-08-20)Protein crystals populate diverse conformational ensembles. Despite much evidence that there is widespread conformational polymorphism in protein side chains, most of the xray crystallography data are modelled by single ... -
Protein Structure Elastic Network Models and the Rank 3 Positive Semidefinite Matrix Manifold
(University of Waterloo, 2019-01-09)This thesis is a contribution to the study of protein dynamics using elastic network models (ENMs). An ENM is an abstraction of a protein structure where inter-atomic interactions are assumed to be modelled by a Hookean ... -
Structural characterization and engineering of Adnectin inclusion bodies
(University of Waterloo, 2022-08-15)Protein aggregation is a fundamental process occurring as a response to aging, disease, protein overexpression and in many areas of biotechnology and medical applications. There has been much recent progress in determining ... -
Structure-aided detection of functional innovation in protein phylogenies
(University of Waterloo, 2016-01-19)Detection of positive selection in proteins is both a common and powerful approach for investigating the molecular basis of adaptation. In this thesis, I explore the use of protein three- dimensional (3D) structure to ...