Discovering Protein Sequence-Structure Motifs and Two Applications to Structural Prediction
Abstract
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.
Collections
Cite this version of the work
Thomas Cheuk Kai Tang
(2004).
Discovering Protein Sequence-Structure Motifs and Two Applications to Structural Prediction. UWSpace.
http://hdl.handle.net/10012/1188
Other formats
Related items
Showing items related by title, author, creator and subject.
-
Robotic stacking: structurally informed free-form timber structure system using standard and non-standard components
Falamarzi Khanehzenyani, Zahra (University of Waterloo, 2020-04-30)This thesis is based on the hypothesis that the synchronization of digital design and robotic fabrication can result in new architectural possibilities. The research investigates differentiation and variability in the ... -
Design of efficient block-sparse data structures and associated tensor multiplications for applications in Cluster in Molecule electronic structure calculations
Liu, Haobo (University of Waterloo, 2022-08-18)The Cluster-in-molecule approach (CiM) is one of the most popular methods in electronic structure calculations for medium to large molecules and systems. The Nooijen group is currently developing a new CiM approach using ... -
Structural investigation of a new cadmium coordination compound prepared by sonochemical process: Crystal structure, Hirshfeld surface, thermal, TD-DFT and NBO analyses
Masoudiasl, A.; Montazerozohori, M.; Joohari, S.; Taghizadeh, L.; Mahmoudi, G.; Assoud, A. (Elsevier, 2019-04)A new nanostructured cadmium complex containing a tridentate Schiff base ligand was sonochemically synthesized and characterized by XRPD, FT/IR, NMR, and single crystal X-ray crystallography. Structural data showed that ...