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Dans, P.D.; Darré, L.; Machado, M.R.; Zeida, A.; Brandner, A.F.; Pantano, S. "Assessing the accuracy of the SIRAH force field to model DNA at coarse grain level" (2013) 8th Brazilian Symposium on Bioinformatics, BSB 2013. 8213 LNBI:71-81
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Abstract:

We present a comparison between atomistic and coarse grain models for DNA developed in our group, which we introduce here with the name SIRAH. Molecular dynamics of DNA fragments performed using implicit and explicit solvation approaches show good agreement in structural and dynamical features with published state of the art atomistic simulations of double stranded DNA (using Amber and Charmm force fields). The study of the multi-microsecond timescale results in counterion condensation on DNA, in coincidence with high-resolution X-ray crystals. This result indicates that our model for solvation is able to correctly reproduce ionic strength effects, which are very difficult to capture by CG schemes. © 2013 Springer International Publishing.

Registro:

Documento: Artículo
Título:Assessing the accuracy of the SIRAH force field to model DNA at coarse grain level
Autor:Dans, P.D.; Darré, L.; Machado, M.R.; Zeida, A.; Brandner, A.F.; Pantano, S.
Ciudad:Recife
Filiación:Institut Pasteur de Montevideo, Mataojo 2020, 11400, Uruguay
Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac, 10, 08028 Barcelona, Spain
Department of Chemistry, King's College London, London, United Kingdom
Deptartamento de Qca. Inorgánica, Analítica Y Química-Física, Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires, C1428EHA Buenos Aires, Argentina
Palabras clave:counterions; flexibility; Molecular dynamics; narrowing; nucleic acids; simulations; WT4; Counterions; flexibility; narrowing; simulations; WT4; DNA; Ionic strength; Molecular dynamics; Nucleic acids; Solvation; Bioinformatics
Año:2013
Volumen:8213 LNBI
Página de inicio:71
Página de fin:81
DOI: http://dx.doi.org/10.1007/978-3-319-02624-4_7
Título revista:8th Brazilian Symposium on Bioinformatics, BSB 2013
Título revista abreviado:Lect. Notes Comput. Sci.
ISSN:03029743
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_03029743_v8213LNBI_n_p71_Dans

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Citas:

---------- APA ----------
Dans, P.D., Darré, L., Machado, M.R., Zeida, A., Brandner, A.F. & Pantano, S. (2013) . Assessing the accuracy of the SIRAH force field to model DNA at coarse grain level. 8th Brazilian Symposium on Bioinformatics, BSB 2013, 8213 LNBI, 71-81.
http://dx.doi.org/10.1007/978-3-319-02624-4_7
---------- CHICAGO ----------
Dans, P.D., Darré, L., Machado, M.R., Zeida, A., Brandner, A.F., Pantano, S. "Assessing the accuracy of the SIRAH force field to model DNA at coarse grain level" . 8th Brazilian Symposium on Bioinformatics, BSB 2013 8213 LNBI (2013) : 71-81.
http://dx.doi.org/10.1007/978-3-319-02624-4_7
---------- MLA ----------
Dans, P.D., Darré, L., Machado, M.R., Zeida, A., Brandner, A.F., Pantano, S. "Assessing the accuracy of the SIRAH force field to model DNA at coarse grain level" . 8th Brazilian Symposium on Bioinformatics, BSB 2013, vol. 8213 LNBI, 2013, pp. 71-81.
http://dx.doi.org/10.1007/978-3-319-02624-4_7
---------- VANCOUVER ----------
Dans, P.D., Darré, L., Machado, M.R., Zeida, A., Brandner, A.F., Pantano, S. Assessing the accuracy of the SIRAH force field to model DNA at coarse grain level. Lect. Notes Comput. Sci. 2013;8213 LNBI:71-81.
http://dx.doi.org/10.1007/978-3-319-02624-4_7