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...
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2013
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| Acceso en línea: | https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_03029743_v8213LNBI_n_p71_Dans http://hdl.handle.net/20.500.12110/paper_03029743_v8213LNBI_n_p71_Dans |
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paper:paper_03029743_v8213LNBI_n_p71_Dans2023-06-08T15:28:51Z Assessing the accuracy of the SIRAH force field to model DNA at coarse grain level 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. 2013 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_03029743_v8213LNBI_n_p71_Dans 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 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. |
| 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 |
| publishDate |
2013 |
| url |
https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_03029743_v8213LNBI_n_p71_Dans http://hdl.handle.net/20.500.12110/paper_03029743_v8213LNBI_n_p71_Dans |
| _version_ |
1768542596245749760 |