Rotational Profiler: A Fast, Automated, and Interactive Server to Derive Torsional Dihedral Potentials for Classical Molecular Simulations

Detalhes bibliográficos
Autor(a) principal: Rusu, Victor H.
Data de Publicação: 2020
Outros Autores: Santos, Denys E. S., Poleto, Marcelo D., Galheigo, Marcelo M., Gomes, Antônio T. A., Verli, Hugo, Soares, Thereza A., Lins, Roberto D.
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/57694
Resumo: Fundação Oswaldo Cruz, Instituto Aggeu Magalhães, Recife, Pernambuco, Brasil. Swiss National Supercomputing Centre, Lugano, Ticino, Switzerland. Universidade Federal de Pernambuco, Depatamento de Quimica Fundamental, Recife, PE, Brasil. Universidade Federal de Viçosa, Depatamento de Biologia Geral, Viçosa, Minas Gerais , Brasil. 4 Laboratório Nacional de Computação Científica do Brasil, Petrópolis, Rio de Janeiro Brasil. 5 Universidade Federal do Rio Grande do Sul, Centro de Biotecnologia, Rio Grande do Sul, Brasil.
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spelling Rusu, Victor H.Santos, Denys E. S.Poleto, Marcelo D.Galheigo, Marcelo M.Gomes, Antônio T. A.Verli, HugoSoares, Thereza A.Lins, Roberto D.2023-04-05T15:10:58Z2023-04-05T15:10:58Z2020-12-28RUSU, Victor H.; SANTOS, Denys E. S.; POLETO, Marcelo D.; GALHEIGO, Marcelo M.; GOMES, Antônio T. A.; VERLI, Hugo; SOARES, Thereza A.; LINS, Roberto D.. Rotational Profiler: a fast, automated, and interactive server to derive torsional dihedral potentials for classical molecular simulations. Journal Of Chemical Information And Modeling, [S.L.], v. 60, n. 12, p. 5923-5927, 19 nov. 2020. American Chemical Society (ACS). http://dx.doi.org/10.1021/acs.jcim.0c01168.1549-960Xhttps://www.arca.fiocruz.br/handle/icict/57694engRotational Profiler: A Fast, Automated, and Interactive Server to Derive Torsional Dihedral Potentials for Classical Molecular Simulationsinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFundação Oswaldo Cruz, Instituto Aggeu Magalhães, Recife, Pernambuco, Brasil. Swiss National Supercomputing Centre, Lugano, Ticino, Switzerland. Universidade Federal de Pernambuco, Depatamento de Quimica Fundamental, Recife, PE, Brasil. Universidade Federal de Viçosa, Depatamento de Biologia Geral, Viçosa, Minas Gerais , Brasil. 4 Laboratório Nacional de Computação Científica do Brasil, Petrópolis, Rio de Janeiro Brasil. 5 Universidade Federal do Rio Grande do Sul, Centro de Biotecnologia, Rio Grande do Sul, Brasil.Rotational Profiler provides an analytical algorithm to compute sets of classical torsional dihedral parameters by fitting an empirical energy profile to a reference one that can be obtained experimentally or by quantum-mechanical methods. The resulting profiles are compatible with the functional forms in the most widely used biomolecular force fields (e.g., GROMOS, AMBER, OPLS, and CHARMM). The linear least-squares regression method is used to generate sets of parameters that best satisfy the fitting. Rotational Profiler is free to use, analytical, and force field/package independent. The formalism is herein described, and its usage, in an interactive and automated manner, is made available as a Web server at http://rotprof.lncc.br.AlgorithmsComputersLeast-Squares Analysisinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-83088https://www.arca.fiocruz.br/bitstream/icict/57694/1/license.txt7b043faf2a6ad46e5344ca8d54801d8cMD51ORIGINALRotational Profiler A Fast, Automated, and Interactive Server to Derive Torsional Dihedral Potentials for Classical Molecular Simulations.pdfRotational Profiler A Fast, Automated, and Interactive Server to Derive Torsional Dihedral Potentials for Classical Molecular Simulations.pdfapplication/pdf2273128https://www.arca.fiocruz.br/bitstream/icict/57694/2/Rotational%20Profiler%20A%20Fast%2c%20Automated%2c%20and%20Interactive%20Server%20to%20Derive%20Torsional%20Dihedral%20Potentials%20for%20Classical%20Molecular%20Simulations.pdf6bd198a250ab9a4d9b59c56deec85b0dMD52icict/576942023-05-22 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dc.title.en_US.fl_str_mv Rotational Profiler: A Fast, Automated, and Interactive Server to Derive Torsional Dihedral Potentials for Classical Molecular Simulations
title Rotational Profiler: A Fast, Automated, and Interactive Server to Derive Torsional Dihedral Potentials for Classical Molecular Simulations
spellingShingle Rotational Profiler: A Fast, Automated, and Interactive Server to Derive Torsional Dihedral Potentials for Classical Molecular Simulations
Rusu, Victor H.
Algorithms
Computers
Least-Squares Analysis
title_short Rotational Profiler: A Fast, Automated, and Interactive Server to Derive Torsional Dihedral Potentials for Classical Molecular Simulations
title_full Rotational Profiler: A Fast, Automated, and Interactive Server to Derive Torsional Dihedral Potentials for Classical Molecular Simulations
title_fullStr Rotational Profiler: A Fast, Automated, and Interactive Server to Derive Torsional Dihedral Potentials for Classical Molecular Simulations
title_full_unstemmed Rotational Profiler: A Fast, Automated, and Interactive Server to Derive Torsional Dihedral Potentials for Classical Molecular Simulations
title_sort Rotational Profiler: A Fast, Automated, and Interactive Server to Derive Torsional Dihedral Potentials for Classical Molecular Simulations
author Rusu, Victor H.
author_facet Rusu, Victor H.
Santos, Denys E. S.
Poleto, Marcelo D.
Galheigo, Marcelo M.
Gomes, Antônio T. A.
Verli, Hugo
Soares, Thereza A.
Lins, Roberto D.
author_role author
author2 Santos, Denys E. S.
Poleto, Marcelo D.
Galheigo, Marcelo M.
Gomes, Antônio T. A.
Verli, Hugo
Soares, Thereza A.
Lins, Roberto D.
author2_role author
author
author
author
author
author
author
dc.contributor.author.fl_str_mv Rusu, Victor H.
Santos, Denys E. S.
Poleto, Marcelo D.
Galheigo, Marcelo M.
Gomes, Antônio T. A.
Verli, Hugo
Soares, Thereza A.
Lins, Roberto D.
dc.subject.en.en_US.fl_str_mv Algorithms
Computers
Least-Squares Analysis
topic Algorithms
Computers
Least-Squares Analysis
description Fundação Oswaldo Cruz, Instituto Aggeu Magalhães, Recife, Pernambuco, Brasil. Swiss National Supercomputing Centre, Lugano, Ticino, Switzerland. Universidade Federal de Pernambuco, Depatamento de Quimica Fundamental, Recife, PE, Brasil. Universidade Federal de Viçosa, Depatamento de Biologia Geral, Viçosa, Minas Gerais , Brasil. 4 Laboratório Nacional de Computação Científica do Brasil, Petrópolis, Rio de Janeiro Brasil. 5 Universidade Federal do Rio Grande do Sul, Centro de Biotecnologia, Rio Grande do Sul, Brasil.
publishDate 2020
dc.date.issued.fl_str_mv 2020-12-28
dc.date.accessioned.fl_str_mv 2023-04-05T15:10:58Z
dc.date.available.fl_str_mv 2023-04-05T15:10:58Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
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status_str publishedVersion
dc.identifier.citation.fl_str_mv RUSU, Victor H.; SANTOS, Denys E. S.; POLETO, Marcelo D.; GALHEIGO, Marcelo M.; GOMES, Antônio T. A.; VERLI, Hugo; SOARES, Thereza A.; LINS, Roberto D.. Rotational Profiler: a fast, automated, and interactive server to derive torsional dihedral potentials for classical molecular simulations. Journal Of Chemical Information And Modeling, [S.L.], v. 60, n. 12, p. 5923-5927, 19 nov. 2020. American Chemical Society (ACS). http://dx.doi.org/10.1021/acs.jcim.0c01168.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/57694
dc.identifier.issn.en_US.fl_str_mv 1549-960X
identifier_str_mv RUSU, Victor H.; SANTOS, Denys E. S.; POLETO, Marcelo D.; GALHEIGO, Marcelo M.; GOMES, Antônio T. A.; VERLI, Hugo; SOARES, Thereza A.; LINS, Roberto D.. Rotational Profiler: a fast, automated, and interactive server to derive torsional dihedral potentials for classical molecular simulations. Journal Of Chemical Information And Modeling, [S.L.], v. 60, n. 12, p. 5923-5927, 19 nov. 2020. American Chemical Society (ACS). http://dx.doi.org/10.1021/acs.jcim.0c01168.
1549-960X
url https://www.arca.fiocruz.br/handle/icict/57694
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
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