Protein Folding Implementation of Stochastic and Deterministic Algorithms using the twodimensional HP Model for Computer Simulation of the Protein Folding Process

Examensarbete för kandidatexamen

Please use this identifier to cite or link to this item: https://hdl.handle.net/20.500.12380/198977
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Type: Examensarbete för kandidatexamen
Bachelor Thesis
Title: Protein Folding Implementation of Stochastic and Deterministic Algorithms using the twodimensional HP Model for Computer Simulation of the Protein Folding Process
Authors: Anker, Malin
Andersson, Simon
Hammar, Tor
Herbertsson, Sebastian
Forsberg, Tobias
Radway, Alexander
Abstract: In nature, proteins are often found to instantly fold into the configuration with the lowest amount of free energy. Due to the complexity of this process, it is today still unknown exactly how it occurs. Since proteins have crucial roles in essentially all biological processes, this is an important problem within structural biology. Computational methods can be used to simulate the problem and a large variety of algorithms have been introduced in the field. Using a widely studied abstraction of this problem, the two-dimensional HP model, this thesis studies the following combinatorial, stochastic and deterministic algorithms: Exhaustive Search, Random Walk, Monte Carlo, Ant Colony Optimization and Zipping and Assembly by Dynamic Programming. The mechanisms, efficiency and results of these algorithms are evaluated and discussed. Even this simplified version of the problem proves to be challenging and gives interesting insights into principles of the protein folding problem.
Keywords: Data- och informationsvetenskap;Computer and Information Science
Issue Date: 2014
Publisher: Chalmers tekniska högskola / Institutionen för data- och informationsteknik (Chalmers)
Chalmers University of Technology / Department of Computer Science and Engineering (Chalmers)
URI: https://hdl.handle.net/20.500.12380/198977
Collection:Examensarbeten för kandidatexamen // Bachelor Theses



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