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Please use this identifier to cite or link to this item: http://hdl.handle.net/1974/1789

Title: Multi-Regional Analysis of Contact Maps for Protein Structure Prediction
Authors: Ahmed, Hazem Radwan A.

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Keywords: Protein Structure
Contact Map
Sequence Similarity
Protein Homology
Issue Date: 2009
Series/Report no.: Canadian theses
Abstract: 1D protein sequences, 2D contact maps and 3D structures are three different representational levels of detail for proteins. Predicting protein 3D structures from their 1D sequences remains one of the complex challenges of bioinformatics. The "Divide and Conquer" principle is applied in our research to handle this challenge, by dividing it into two separate yet dependent subproblems, using a Case-Based Reasoning (CBR) approach. Firstly, 2D contact maps are predicted from their 1D protein sequences; secondly, 3D protein structures are then predicted from their predicted 2D contact maps. We focus on the problem of identifying common substructural patterns of protein contact maps, which could potentially be used as building blocks for a bottom-up approach for protein structure prediction. We further demonstrate how to improve identifying these patterns by combining both protein sequence and structural information. We assess the consistency and the efficiency of identifying common substructural patterns by conducting statistical analyses on several subsets of the experimental results with different sequence and structural information.
Description: Thesis (Master, Computing) -- Queen's University, 2009-04-23 22:01:04.528
URI: http://hdl.handle.net/1974/1789
Appears in Collections:Queen's Graduate Theses and Dissertations
School of Computing Graduate Theses

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