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Investigation of an immune algorithm and differential evolution to study folding of model proteins

Bennett, Andrew James (2010)
Ph.D. thesis, University of Birmingham.

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The application of computational search techniques to global optimisation problems is becoming increasingly popular. Search techniques have been used to study the folding of model proteins, with the aim of accurately predicting the native state of a protein from its amino acid sequence. Through modelling, knowledge of the folding process can be obtained. In this thesis, two search techniques have been applied to a variety of protein models. The development and application of both an Immune algorithm and a Differential Evolution search technique are described, with the aim of finding the lowest energy conformations of coarse-grained, model proteins. Initially, the two-dimensional HP Lattice Bead Model is investigated, followed by three-dimensional models of varying complexity. The HP Lattice Bead and BLN models, on a diamond lattice are considered, as well as the Dynamic lattice Model, using backbone torsion angles to define the structure of the lattice. A modified chain growth constructor is introduced; firstly, to generate the initial population for both search techniques, secondly, to record unoccupied lattice sites of meta-stable conformations to reduce the risk of performing infeasible joint mutations during the mutation phase for the Immune algorithm, and thirdly, to improve the standard of mutations performed by Differential Evolution. A novel profiling system is introduced based on the theory of genealogy and ancestry by recording the parent of each individual. The method is used to track and evaluate the diversity of populations and assess the impact that genetic operators have on this diversity. The aim of applying this system is three fold: to investigate how effective genetic operators are; to allow a greater understanding of the progress of the optimisations; and to assess the strengths and weaknesses of each search technique investigated.

Type of Work:Ph.D. thesis.
Supervisor(s):Johnston, Roy (Professor)
School/Faculty:Colleges (2008 onwards) > College of Engineering & Physical Sciences
Subjects:QD Chemistry
Institution:University of Birmingham
ID Code:499
This unpublished thesis/dissertation is copyright of the author and/or third parties. The intellectual property rights of the author or third parties in respect of this work are as defined by The Copyright Designs and Patents Act 1988 or as modified by any successor legislation. Any use made of information contained in this thesis/dissertation must be in accordance with that legislation and must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the permission of the copyright holder.
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