Comparing protein structures based on their contact maps is an important problem in structural proteomics. Building a system for reconstructing protein tertiary structures from their contact maps is one of the motivations for devising novel contact map comparison algorithms. Several methods that address the contact map comparison problem have been designed which are briefly discussed in this thesis. However, they suggest scoring schemes that do not satisfy the two characteristics of “metricity” and “universality”. In this research we investigate the applicability of the Universal Similarity Metric (USM) to the contact map comparison problem. The USM is an information theoretical measure which is based on the concept of Kolmogorov complexity. The ultimate goal of this research is to use the USM in case-based reasoning system to predict protein structures from their predicted contact maps. The fact that the contact maps that will be used in such a system are the ones which are predicted from the protein sequences and are not noise-free, implies that we should investigate the noise-sensitivity of the USM. This is the first attempt to study the noise-tolerance of the USM. In this research, as the first implementation of the USM we converted the two-dimensional data structures (contact maps) to one-dimensional data structures (strings). The results of this implementation motivated us to circumvent the dimension reduction in our second attempt to implement the USM. Our suggested method in this thesis has the advantage of obtaining a measure which is noise tolerant. We assess the effectiveness of this noise tolerance by testing different USM implementation schemes against noise-contaminated versions of distinguished data-sets. / Thesis (Master, Computing) -- Queen's University, 2008-09-27 05:53:31.988