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Title:Optimizacija zvijanja proteinov znotraj kubične mreže s pomočjo evolucijskega algoritma in grafične procesne enote : diplomsko delo
Authors:Vipotnik, Matic (Author)
Bošković, Borko (Mentor) More about this mentor... New window
Brest, Janez (Co-mentor)
Files:.pdf UN_Vipotnik_Matic_2020.pdf (748,33 KB)
MD5: EAF18D2F2C2BACDC1E62C782074A8AD5
Work type:Bachelor thesis/paper (mb11)
Typology:2.11 - Undergraduate Thesis
Organization:FERI - Faculty of Electrical Engineering and Computer Science
Abstract:V diplomskem delu smo implementirali algoritem za optimizacijo zvijanja proteinov znotraj modela HP. Algoritem na centralno procesni enoti porabi veliko časa, da protein zvije v optimalno strukturo. Zato smo algoritem prilagodili, da se izvaja na grafični procesni enoti. Učinkovitost algoritma smo analizirali na znanih sekvencah iz literature. S pomočjo algoritma, ki se je izvajal na grafični procesni enoti smo v povprečju dosegli 10,2 - kratno pohitritev v primerjavi z algoritmom, ki se izvaja na centralno procesni enoti.
Keywords:zvijanje proteinov, CUDA, optimizacija, evolucijski algoritem
Year of publishing:2020
Place of performance:Maribor
Publisher:[M. Vipotnik]
Number of pages:X, 30 f.
COBISS_ID:35582723 New window
Categories:KTFMB - FERI
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License:CC BY-NC-ND 4.0, Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
Description:The most restrictive Creative Commons license. This only allows people to download and share the work for no commercial gain and for no other purposes.
Licensing start date:16.09.2020

Secondary language

Title:Protein folding optimization within a cubic lattice by using an evolutionary algorithm and a graphics processing unit
Abstract:In the thesis, we implemented an algorithm for protein folding optimization within the HP model. The algorithm on the central processing unit takes a long time to fold protein into an optimal structure. Therefore, we adapted the algorithm to run on a graphics processing unit. The efficiency of the algorithm was analyzed on well-known sequences from the literature. With the help of an algorithm that was running on a graphics processing unit, we achieved on average speedup of 10,2 in compared to algorithm running on central processing unit.
Keywords:protein folding, CUDA, optimization, evolutionary algorithm


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