Contributions to the study of the protein folding problem using bioinspired computation and molecular dynamics
The Protein Folding Problem (PFP) is considered one of the most important open cha- llenges in Biology and Bioinformatics. In this thesis, a novel approach for simulating the protein folding pathways is proposed where, instead using the three-dimensional structure of the protein, the folding states...
| Autor principal: | Benítez, César Manuel Vargas |
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| Idioma: | Inglês |
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Universidade Tecnológica Federal do Paraná
2015
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riut-1-12112015-06-03T06:00:21Z Contributions to the study of the protein folding problem using bioinspired computation and molecular dynamics Benítez, César Manuel Vargas Lopes, Heitor Silvério Bioinformática Computação evolutiva Processamento paralelo (Computadores) Automato celular Dinâmica molecular Métodos de simulação Engenharia elétrica Bioinformatics Evolutionary computation Parallel processing (Electronic computer) Cellular automata Molecular dynamics Simulation methods Electric engineering The Protein Folding Problem (PFP) is considered one of the most important open cha- llenges in Biology and Bioinformatics. In this thesis, a novel approach for simulating the protein folding pathways is proposed where, instead using the three-dimensional structure of the protein, the folding states are represented by Contact Maps (CM). A two-dimensional Cellular Automata (2D-CA) evolver is used to simulate the fol- ding process, where each configuration represents a folding state and it is obtained according to its predecessor and a transition rule. Since finding transition rules for simulating a dynamic behavior is a very difficult task, it is proposed a distributed Gene-Expression Programming (GEP)-based approach, called pGEP-CA. Specific fit- ness functions, based on similarity and symmetry measures, are proposed. Futhermore, a heterogeneous parallel Ecology-inspired algorithm is proposed. This algorithm, called pECO, is used for reconstructing the structures from the CMs, using the 3D-AB off-lattice model. Moreover, to the best of our knowledge, it is presented the first application of Molecular Dynamics (MD) to the PFP, using the same model of proteins. Experiments were done to evaluate the adequacy of the proposed approaches. Also, a brief analysis of the load balancing of the parallel architectures is presented. Results show that the approaches obtained coherent results, suggesting their adequacy for the problem. The induced transition rules by the pGEP-CA are able to generate 2D-CA that represent CMs correctly. Concerning the pECO approach, results show that the combination of concurrent evolutionary approaches took advantage of both the coevolution effect and the different search strategies. In addition, it can be observed that the MD approach is capable of displaying biological features such as the hydrophobic core formation and the protein breathing motion. Furthermore, it is observed that parallel processing was not only justified but also essential for obtaining results in reasonable processing time. Finally, concluding remarks and several research directions for future works are presented. O Problema de Dobramento de Proteínas (PDP) é considerado um dos desafios abertos mais importantes da Biologia e Bioinformática. Nesta tese, uma nova abordagem para simular os pathways de dobramento de proteínas é proposta onde, ao invés de utilizar a estrutura tridimensional da proteína, os estados de dobramento são representados por Mapas de Contatos (MC). Autômatos Celulares bidimensionais (2D-CA) são utilizados para simular o processo de dobramento, onde cada configuração representa um estado de dobramento e é obtida em relação ao seu estado predecessor e uma regra de transição. Determinar uma regra de transição para um dado comportamento dinâmico representa uma tarefa complexa. Portanto, é apresentada uma abordagem distribuida baseada em Programação de Expressão Gênica, chamada pGEP-CA. Funções de fitness específicas, baseadas em medidas de similaridade e simetria, são propostas. Também, um algoritmo heterogêneo paralelo Ecologicamente-inspirado é proposto. Este algoritmo, chamado pECO, é utilizado na reconstrução de estruturas a partir de MCs, usando o modelo 3D-AB off-lattice. De acordo com o nosso conhecimento, é apresentada a primeira aplicação de Dinâmica Molecular (DM) ao PFP, usando o mesmo modelo de proteínas. Experimentos foram realizados para verificar a adequabilidade das abordagens propostas. Além disto, uma breve análise sobre o balanceamento de carga de processamento das arquiteturas paralelas é apresentada. Os resultados mostram que as abordagens obtiveram resultados coerentes, sugerindo que são adequadas para o problema. As regras de transição induzidas pelo pGEP-CA são capazes de gerar 2D-CA que representam MCs corretamente. Sobre a abordagem pECO, os resultados demonstram que a combinação de abordagens evolucionárias concorrentes se beneficia do efeito da coevolução e das diferentes estratégias de busca. Além disto, pode ser observado que a abordagem de DM é capaz de levar a conformações que mimetizam propriedades biológicas, como a formação do núcleo hidrofóbico e os movimentos de respiração (breathing) das proteínas. Também foi observado que o processamento paralelo é essencial, permitindo a obtenção de resultados em tempos de processamento razoáveis. Finalmente, as conclusões e diversas direções de pesquisa são apresentadas. 2015-06-02T13:35:50Z 2015-06-02T13:35:50Z 2015-04-27 doctoralThesis BENÍTEZ, César Manuel Vargas. Contributions to the study of the protein folding problem using bioinspired computation and molecular dynamics. 2015. 193 f. Dissertação (Mestrado em Engenharia Elétrica e Informática Industrial) – Universidade Tecnológica Federal do Paraná, Curitiba, 2015. http://repositorio.utfpr.edu.br/jspui/handle/1/1211 eng application/pdf Universidade Tecnológica Federal do Paraná Curitiba Programa de Pós-Graduação em Engenharia Elétrica e Informática Industrial |
| institution |
Universidade Tecnológica Federal do Paraná |
| collection |
RIUT |
| language |
Inglês |
| topic |
Bioinformática Computação evolutiva Processamento paralelo (Computadores) Automato celular Dinâmica molecular Métodos de simulação Engenharia elétrica Bioinformatics Evolutionary computation Parallel processing (Electronic computer) Cellular automata Molecular dynamics Simulation methods Electric engineering |
| spellingShingle |
Bioinformática Computação evolutiva Processamento paralelo (Computadores) Automato celular Dinâmica molecular Métodos de simulação Engenharia elétrica Bioinformatics Evolutionary computation Parallel processing (Electronic computer) Cellular automata Molecular dynamics Simulation methods Electric engineering Benítez, César Manuel Vargas Contributions to the study of the protein folding problem using bioinspired computation and molecular dynamics |
| description |
The Protein Folding Problem (PFP) is considered one of the most important open cha- llenges in Biology and Bioinformatics. In this thesis, a novel approach for simulating the protein folding pathways is proposed where, instead using the three-dimensional structure of the protein, the folding states are represented by Contact Maps (CM). A two-dimensional Cellular Automata (2D-CA) evolver is used to simulate the fol- ding process, where each configuration represents a folding state and it is obtained according to its predecessor and a transition rule. Since finding transition rules for simulating a dynamic behavior is a very difficult task, it is proposed a distributed Gene-Expression Programming (GEP)-based approach, called pGEP-CA. Specific fit- ness functions, based on similarity and symmetry measures, are proposed. Futhermore, a heterogeneous parallel Ecology-inspired algorithm is proposed. This algorithm, called pECO, is used for reconstructing the structures from the CMs, using the 3D-AB off-lattice model. Moreover, to the best of our knowledge, it is presented the first application of Molecular Dynamics (MD) to the PFP, using the same model of proteins. Experiments were done to evaluate the adequacy of the proposed approaches. Also, a brief analysis of the load balancing of the parallel architectures is presented. Results show that the approaches obtained coherent results, suggesting their adequacy for the problem. The induced transition rules by the pGEP-CA are able to generate 2D-CA that represent CMs correctly. Concerning the pECO approach, results show that the combination of concurrent evolutionary approaches took advantage of both the coevolution effect and the different search strategies. In addition, it can be observed that the MD approach is capable of displaying biological features such as the hydrophobic core formation and the protein breathing motion. Furthermore, it is observed that parallel processing was not only justified but also essential for obtaining results in reasonable processing time. Finally, concluding remarks and several research directions for future works are presented. |
| format |
Tese |
| author |
Benítez, César Manuel Vargas |
| author_sort |
Benítez, César Manuel Vargas |
| title |
Contributions to the study of the protein folding problem using bioinspired computation and molecular dynamics |
| title_short |
Contributions to the study of the protein folding problem using bioinspired computation and molecular dynamics |
| title_full |
Contributions to the study of the protein folding problem using bioinspired computation and molecular dynamics |
| title_fullStr |
Contributions to the study of the protein folding problem using bioinspired computation and molecular dynamics |
| title_full_unstemmed |
Contributions to the study of the protein folding problem using bioinspired computation and molecular dynamics |
| title_sort |
contributions to the study of the protein folding problem using bioinspired computation and molecular dynamics |
| publisher |
Universidade Tecnológica Federal do Paraná |
| publishDate |
2015 |
| citation |
BENÍTEZ, César Manuel Vargas. Contributions to the study of the protein folding problem using bioinspired computation and molecular dynamics. 2015. 193 f. Dissertação (Mestrado em Engenharia Elétrica e Informática Industrial) – Universidade Tecnológica Federal do Paraná, Curitiba, 2015. |
| url |
http://repositorio.utfpr.edu.br/jspui/handle/1/1211 |
| _version_ |
1805302534104940544 |
| score |
10,814766 |