Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS

Detalhes bibliográficos
Autor(a) principal: Vieira, Ivo Henrique Provensi
Data de Publicação: 2023
Outros Autores: Botelho, Eduardo Buganemi, Gomes, Thales Junior de Souza, Kist, Roger, Caceres, Rafael Andrade, Zanchi, Fernando Berton
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
DOI: 10.1186/s12859-023-05234-y
Texto Completo: https://arca.fiocruz.br/handle/icict/70630
Resumo: CAPES
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spelling Vieira, Ivo Henrique ProvensiBotelho, Eduardo BuganemiGomes, Thales Junior de SouzaKist, RogerCaceres, Rafael AndradeZanchi, Fernando Berton2025-05-25T21:52:45Z2025-05-25T21:52:45Z2023VIEIRA, Ivo Henrique Provensi et al. Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS. BMC Bioinformatics, v. 24, n. 107, p. 1-12, 22 Mar. 2023.1471-2105https://arca.fiocruz.br/handle/icict/7063010.1186/s12859-023-05234-yCAPESFundação Oswaldo Cruz. Fiocruz Rondônia. Laboratório de Bioinformática e Química Medicinal. Porto Velho, RO, Brasil.Fundação Oswaldo Cruz. Fiocruz Rondônia. Laboratório de Bioinformática e Química Medicinal. Porto Velho, RO, Brasil.Fundação Oswaldo Cruz. Fiocruz Rondônia. Laboratório de Bioinformática e Química Medicinal. Porto Velho, RO, Brasil.Universidade Federal de Ciências da Saúde de Porto Alegre. Porto Alegre, RS, Brasil.Universidade Federal de Ciências da Saúde de Porto Alegre. Porto Alegre, RS, Brasil.Fundação Oswaldo Cruz. Fiocruz Rondônia. Laboratório de Bioinformática e Química Medicinal. Porto Velho, RO, Brasil / Fundação Universidade Federal de Rondônia. Programa de Pós-Graduação em Biologia Experimental. Porto Velho, RO, Brasil / Fundação Oswaldo Cruz. Fiocruz Rondônia. Porto Velho, RO, Brasil / Fundação Oswaldo Cruz. Fiocruz Rondônia. Instituto Nacional de Epidemiologia na Amazônia Ocidental. Porto Velho, RO, Brasil / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Programa de Pós-graduação Stricto sensu em Biologia Computacional e Sistemas. Rio de Janeiro, RJ, Brasil.Background: The molecular dynamics is an approach to obtain kinetic and thermodynamic characteristics of biomolecular structures. The molecular dynamics simulation softwares are very useful, however, most of them are used in command line form and continue with the same common implementation difficulties that plague researchers who are not computer specialists. Results: Here, we have developed the VisualDynamics—a WEB tool developed to automate biological simulations performed in Gromacs using a graphical interface to make molecular dynamics simulation user-friendly task. In this new application the researcher can submit a simulation of the protein in the free form or complexed with a ligand. Can also download the graphics analysis and log files at the end of the simulation. Conclusions: VisualDynamics is a tool that will accelerate implementations and learning in the area of molecular dynamics simulation. Freely available at https:// visua ldyna mics. fiocr uz. br/ login, is supported by all major web browsers. VisualDynamics was developed with Flask, which is a Python-based free and open-source framework for web development. 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dc.title.none.fl_str_mv Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS
title Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS
spellingShingle Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS
Vieira, Ivo Henrique Provensi
Molecular dynamics
WEB
GUI
GROMACS
Python
Molecular dynamics
WEB
title_short Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS
title_full Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS
title_fullStr Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS
title_full_unstemmed Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS
title_sort Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS
author Vieira, Ivo Henrique Provensi
author_facet Vieira, Ivo Henrique Provensi
Botelho, Eduardo Buganemi
Gomes, Thales Junior de Souza
Kist, Roger
Caceres, Rafael Andrade
Zanchi, Fernando Berton
author_role author
author2 Botelho, Eduardo Buganemi
Gomes, Thales Junior de Souza
Kist, Roger
Caceres, Rafael Andrade
Zanchi, Fernando Berton
author2_role author
author
author
author
author
dc.contributor.author.fl_str_mv Vieira, Ivo Henrique Provensi
Botelho, Eduardo Buganemi
Gomes, Thales Junior de Souza
Kist, Roger
Caceres, Rafael Andrade
Zanchi, Fernando Berton
dc.subject.en.none.fl_str_mv Molecular dynamics
WEB
GUI
GROMACS
Python
topic Molecular dynamics
WEB
GUI
GROMACS
Python
Molecular dynamics
WEB
dc.subject.decs.none.fl_str_mv Molecular dynamics
WEB
description CAPES
publishDate 2023
dc.date.issued.fl_str_mv 2023
dc.date.accessioned.fl_str_mv 2025-05-25T21:52:45Z
dc.date.available.fl_str_mv 2025-05-25T21:52:45Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.citation.fl_str_mv VIEIRA, Ivo Henrique Provensi et al. Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS. BMC Bioinformatics, v. 24, n. 107, p. 1-12, 22 Mar. 2023.
dc.identifier.uri.fl_str_mv https://arca.fiocruz.br/handle/icict/70630
dc.identifier.issn.none.fl_str_mv 1471-2105
dc.identifier.doi.none.fl_str_mv 10.1186/s12859-023-05234-y
identifier_str_mv VIEIRA, Ivo Henrique Provensi et al. Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS. BMC Bioinformatics, v. 24, n. 107, p. 1-12, 22 Mar. 2023.
1471-2105
10.1186/s12859-023-05234-y
url https://arca.fiocruz.br/handle/icict/70630
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
instname_str Fundação Oswaldo Cruz (FIOCRUZ)
instacron_str FIOCRUZ
institution FIOCRUZ
reponame_str Repositório Institucional da FIOCRUZ (ARCA)
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