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Title: Ab initio protein fold prediction using evolutionary algorithms
Author: Djurdjević, Dušan
Awarding Body: University of Edinburgh
Current Institution: University of Edinburgh
Date of Award: 2006
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A comprehensive study was undertaken for ab initio protein fold prediction using a fully atomistic protein model and a physicochemical potential. Twenty four EA designs where initially assessed on polyalanine, a prototypical α-helical polypeptide.  Design aspects varied include the encoding alphabet, crossover operator, replacement strategy and selection strategy. By undertaking a comprehensive parameter study, the best performing designs and associated control parameter values were identified for polyalanine. The scaling between the performance and polyalinine size was also identified for these best designs. This initial study was followed by a similar parametric study for met-enkephalin, a five residue polypeptide that has long been used as a de facto standard test case for protein structure prediction algorithms. It was found that the control parameter scalings identified from the polyalinine study were transferable to this real protein, and that the EA is superior to all existing ab initio approaches for met-enkephalin. The best design was finally applied to a series of real proteins ranging in size up to 45 residues to more generally assess the EA’s performance. The thesis is concluded with consideration of the future work required to extend the EA to larger proteins and ab initio structure prediction for non-native environments such as at interfaces, which are of relevance to, for example, biosensors.
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available