Discovering Protein Sequence-Structure Motifs and Two Applications to Structural Prediction
MetadataShow full item record
This thesis investigates the correlations between short protein peptide sequences and local tertiary structures. In particular, it introduces a novel algorithm for partitioning short protein segments into clusters of local sequence-structure motifs, and demonstrates that these motif clusters contain useful structural information via two applications to structural prediction. The first application utilizes motif clusters to predict local protein tertiary structures. A novel dynamic programming algorithm that performs comparably with some of the best existing algorithms is described. The second application exploits the capability of motif clusters in recognizing regular secondary structures to improve the performance of secondary structure prediction based on Support Vector Machines. Empirical results show significant improvement in overall prediction accuracy with no performance degradation in any specific aspect being measured. The encouraging results obtained illustrate the great potential of using local sequence-structure motifs to tackle protein structure predictions and possibly other important problems in computational biology.
Cite this work
Thomas Cheuk Kai Tang (2004). Discovering Protein Sequence-Structure Motifs and Two Applications to Structural Prediction. UWSpace. http://hdl.handle.net/10012/1188
Showing items related by title, author, creator and subject.
Jensen, Kyle (University of Waterloo, 2015-05-13)This thesis investigates how to reduce the raw materials invested in a building, specifically in the structural aspect of its construction, and in so doing decrease the embodied energy required to build a structure. Geometric ...
The Ten Stone Ranges Structural Complex of the central Mackenzie Mountains fold-and-thrust belt: a structural analysis with implications on the Plateau Fault and regional detachment level MacDonald, Justin (University of Waterloo, 2009-09-01)The Cordilleran Orogen affected majority of the western margin of ancient continental North America in the Cretaceous, which is well recorded in the Foreland Belt. The Mackenzie Mountains fold-and-thrust belt is located ...
The effect of peat structure on the spatial distribution of biogenic gases within bogs: EFFECT OF PEAT STRUCTURE ON BIOGENIC GAS Comas, Xavier; Kettridge, Nicholas; Binley, Andrew; Slater, Lee; Parsekian, Andrew; Baird, Andy J.; Strack, Maria; Waddington, James M. (Wiley, 2014-10-30)Northern peatlands are a large source of atmospheric methane (CH4) and both a source and a sink of atmospheric carbon dioxide (CO2). The rate and temporal variability in gas exchanges with peat soils is directly related ...