Smart execution of molecular docking simulations of a fully-flexible receptor model

Detalhes bibliográficos
Autor(a) principal: Frantz, Fábio André
Data de Publicação: 2012
Tipo de documento: Dissertação
Idioma: por
Título da fonte: Repositório Institucional PUCRS
Texto Completo: http://hdl.handle.net/10923/1544
Resumo: Molecular docking simulations of Fully-Flexible Receptor (FFR) models are coming of age. However, they demand parallelization of computing activities for their executions and generate huge amounts of data that needs to be analyzed. Many Task Computing (MTC) is an attractive paradigm routinely applied to execute intensive tasks. In this work we propose an environment to execute molecular docking simulations of FFR models to small molecules integrated with an MTC middleware. This environment is based on a new pattern called Self-adapting Multiple Instances (P-SaMI) that provide rules to reduce the number of experiments, providing a Reduced Fully-Flexible Receptor (RFFR) model. The main contribution of this research is to prove that P-SaMI rules can be used on Molecular Docking Simulations through a web environment integrated with an MTC middleware.
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spelling Frantz, Fábio AndréRuiz, Duncan Dubugras Alcoba2013-08-07T18:42:49Z2013-08-07T18:42:49Z2012http://hdl.handle.net/10923/1544Molecular docking simulations of Fully-Flexible Receptor (FFR) models are coming of age. However, they demand parallelization of computing activities for their executions and generate huge amounts of data that needs to be analyzed. Many Task Computing (MTC) is an attractive paradigm routinely applied to execute intensive tasks. In this work we propose an environment to execute molecular docking simulations of FFR models to small molecules integrated with an MTC middleware. This environment is based on a new pattern called Self-adapting Multiple Instances (P-SaMI) that provide rules to reduce the number of experiments, providing a Reduced Fully-Flexible Receptor (RFFR) model. The main contribution of this research is to prove that P-SaMI rules can be used on Molecular Docking Simulations through a web environment integrated with an MTC middleware.Simulações de docagem molecular com modelos de Receptores Totalmente Flexíveis (FFR) estão adquirindo maturidade. No entanto, isto demanda atividades computacionais de paralelização para geração e execução de grande volume de dados que precisam ser analizados. Computação multi-tarefa é um paradigma atrativo e que vem sendo aplicado frequentemente para executar tarefas intensivas. Neste trabalho propomos um ambiente para executar simulações de docagem molecular no modelo FFR com pequenas moléculas integradas a um componente MTC. Este ambiente é baseado no padrão Múltiplas Instâncias Autoadaptáveis (P-SaMI) que possui regras para redução do número de experimentos, provendo um modelo de Receptores Totalmente Flexíveis Reduzido (RFFR). A principal contribuição desta pesquisa está na comprovação de que as regras do P-SaMI podem ser usadas em Simulações de Docagem Molecular através de um ambiente web integrado com um componente MTC.Made available in DSpace on 2013-08-07T18:42:49Z (GMT). No. of bitstreams: 1 000439095-Texto+Completo-0.pdf: 3289381 bytes, checksum: eb6fc534e5a9d631dbafb97aa0a9c407 (MD5) Previous issue date: 2012Pontifícia Universidade Católica do Rio Grande do SulPorto AlegreINFORMÁTICABANCO DE DADOSBIOLOGIA MOLECULARBIOLOGIA COMPUTACIONALSmart execution of molecular docking simulations of a fully-flexible receptor modelinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/masterThesisPontifícia Universidade Católica do Rio Grande do SulFaculdade de InformáticaPrograma de Pós-Graduação em Ciência da ComputaçãoMestrado2012porreponame:Repositório Institucional PUCRSinstname:Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS)instacron:PUC_RSinfo:eu-repo/semantics/openAccessTEXT000439095-Texto+Completo-0.pdf.txt000439095-Texto+Completo-0.pdf.txtExtracted texttext/plain163876http://meriva.pucrs.br:8080/jspui/bitstream/10923/1544/3/000439095-Texto%2BCompleto-0.pdf.txt9aaa91244a49ade852131d2c0bed1741MD53ORIGINAL000439095-Texto+Completo-0.pdfTexto Completoapplication/pdf3289381http://meriva.pucrs.br:8080/jspui/bitstream/10923/1544/1/000439095-Texto%2BCompleto-0.pdfeb6fc534e5a9d631dbafb97aa0a9c407MD51LICENSElicense.txttext/plain601http://meriva.pucrs.br:8080/jspui/bitstream/10923/1544/2/license.txt3d470ad030ca6782c9f44a1fb7650ec0MD5210923/15442017-09-27 15:49:26.434oai:meriva.pucrs.br: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Repositório InstitucionalPRIhttp://repositorio.pucrs.br/oai/request?verb=Identifyopendoar:27532017-09-27T18:49:26Repositório Institucional PUCRS - Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS)false
dc.title.pt_BR.fl_str_mv Smart execution of molecular docking simulations of a fully-flexible receptor model
title Smart execution of molecular docking simulations of a fully-flexible receptor model
spellingShingle Smart execution of molecular docking simulations of a fully-flexible receptor model
Frantz, Fábio André
INFORMÁTICA
BANCO DE DADOS
BIOLOGIA MOLECULAR
BIOLOGIA COMPUTACIONAL
title_short Smart execution of molecular docking simulations of a fully-flexible receptor model
title_full Smart execution of molecular docking simulations of a fully-flexible receptor model
title_fullStr Smart execution of molecular docking simulations of a fully-flexible receptor model
title_full_unstemmed Smart execution of molecular docking simulations of a fully-flexible receptor model
title_sort Smart execution of molecular docking simulations of a fully-flexible receptor model
author Frantz, Fábio André
author_facet Frantz, Fábio André
author_role author
dc.contributor.author.fl_str_mv Frantz, Fábio André
dc.contributor.advisor1.fl_str_mv Ruiz, Duncan Dubugras Alcoba
contributor_str_mv Ruiz, Duncan Dubugras Alcoba
dc.subject.por.fl_str_mv INFORMÁTICA
BANCO DE DADOS
BIOLOGIA MOLECULAR
BIOLOGIA COMPUTACIONAL
topic INFORMÁTICA
BANCO DE DADOS
BIOLOGIA MOLECULAR
BIOLOGIA COMPUTACIONAL
description Molecular docking simulations of Fully-Flexible Receptor (FFR) models are coming of age. However, they demand parallelization of computing activities for their executions and generate huge amounts of data that needs to be analyzed. Many Task Computing (MTC) is an attractive paradigm routinely applied to execute intensive tasks. In this work we propose an environment to execute molecular docking simulations of FFR models to small molecules integrated with an MTC middleware. This environment is based on a new pattern called Self-adapting Multiple Instances (P-SaMI) that provide rules to reduce the number of experiments, providing a Reduced Fully-Flexible Receptor (RFFR) model. The main contribution of this research is to prove that P-SaMI rules can be used on Molecular Docking Simulations through a web environment integrated with an MTC middleware.
publishDate 2012
dc.date.issued.fl_str_mv 2012
dc.date.accessioned.fl_str_mv 2013-08-07T18:42:49Z
dc.date.available.fl_str_mv 2013-08-07T18:42:49Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/masterThesis
format masterThesis
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/10923/1544
url http://hdl.handle.net/10923/1544
dc.language.iso.fl_str_mv por
language por
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Pontifícia Universidade Católica do Rio Grande do Sul
Porto Alegre
publisher.none.fl_str_mv Pontifícia Universidade Católica do Rio Grande do Sul
Porto Alegre
dc.source.none.fl_str_mv reponame:Repositório Institucional PUCRS
instname:Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS)
instacron:PUC_RS
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reponame_str Repositório Institucional PUCRS
collection Repositório Institucional PUCRS
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