Assessing the accuracy of the SIRAH force field to model DNA at coarse grain level

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...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Dans, P.D., Darré, L., Machado, M.R., Zeida, A., Brandner, A.F., Pantano, S.
Formato:	SER
Materias:	counterions flexibility Molecular dynamics narrowing nucleic acids simulations WT4 Counterions DNA Ionic strength Nucleic acids Solvation Bioinformatics
Acceso en línea:	http://hdl.handle.net/20.500.12110/paper_03029743_v8213LNBI_n_p71_Dans
Aporte de:	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires

id	todo:paper_03029743_v8213LNBI_n_p71_Dans
record_format	dspace
spelling	todo:paper_03029743_v8213LNBI_n_p71_Dans2023-10-03T15:19:33Z Assessing the accuracy of the SIRAH force field to model DNA at coarse grain level Dans, P.D. Darré, L. Machado, M.R. Zeida, A. Brandner, A.F. Pantano, S. counterions flexibility Molecular dynamics narrowing nucleic acids simulations WT4 Counterions flexibility narrowing simulations WT4 DNA Ionic strength Molecular dynamics Nucleic acids Solvation Bioinformatics 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. SER info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_03029743_v8213LNBI_n_p71_Dans
institution	Universidad de Buenos Aires
institution_str	I-28
repository_str	R-134
collection	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic	counterions flexibility Molecular dynamics narrowing nucleic acids simulations WT4 Counterions flexibility narrowing simulations WT4 DNA Ionic strength Molecular dynamics Nucleic acids Solvation Bioinformatics
spellingShingle	counterions flexibility Molecular dynamics narrowing nucleic acids simulations WT4 Counterions flexibility narrowing simulations WT4 DNA Ionic strength Molecular dynamics Nucleic acids Solvation Bioinformatics 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
topic_facet	counterions flexibility Molecular dynamics narrowing nucleic acids simulations WT4 Counterions flexibility narrowing simulations WT4 DNA Ionic strength Molecular dynamics Nucleic acids Solvation Bioinformatics
description	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.
format	SER
author	Dans, P.D. Darré, L. Machado, M.R. Zeida, A. Brandner, A.F. Pantano, S.
author_facet	Dans, P.D. Darré, L. Machado, M.R. Zeida, A. Brandner, A.F. Pantano, S.
author_sort	Dans, P.D.
title	Assessing the accuracy of the SIRAH force field to model DNA at coarse grain level
title_short	Assessing the accuracy of the SIRAH force field to model DNA at coarse grain level
title_full	Assessing the accuracy of the SIRAH force field to model DNA at coarse grain level
title_fullStr	Assessing the accuracy of the SIRAH force field to model DNA at coarse grain level
title_full_unstemmed	Assessing the accuracy of the SIRAH force field to model DNA at coarse grain level
title_sort	assessing the accuracy of the sirah force field to model dna at coarse grain level
url	http://hdl.handle.net/20.500.12110/paper_03029743_v8213LNBI_n_p71_Dans
work_keys_str_mv	AT danspd assessingtheaccuracyofthesirahforcefieldtomodeldnaatcoarsegrainlevel AT darrel assessingtheaccuracyofthesirahforcefieldtomodeldnaatcoarsegrainlevel AT machadomr assessingtheaccuracyofthesirahforcefieldtomodeldnaatcoarsegrainlevel AT zeidaa assessingtheaccuracyofthesirahforcefieldtomodeldnaatcoarsegrainlevel AT brandneraf assessingtheaccuracyofthesirahforcefieldtomodeldnaatcoarsegrainlevel AT pantanos assessingtheaccuracyofthesirahforcefieldtomodeldnaatcoarsegrainlevel
_version_	1807317202691424256

Assessing the accuracy of the SIRAH force field to model DNA at coarse grain level

Ejemplares similares