The DOI matches its Crossref record; 75 of the 75 references it cites were found in a registry or an index.
Martini Coarse-Grained Force Field: Extension to DNA
Open accessAbstract
We systematically parameterized a coarse-grained (CG) model for DNA that is compatible with the Martini force field. The model maps each nucleotide into six to seven CG beads and is parameterized following the Martini philosophy. The CG nonbonded interactions are based on partitioning of the nucleobases between polar and nonpolar solvents as well as base-base potential of mean force calculations. The bonded interactions are fit to single-stranded DNA (ssDNA) atomistic simulations and an elastic network is used to retain double-stranded DNA (dsDNA) and other specific DNA conformations. We present the implementation of the Martini DNA model and demonstrate the properties of individual bases, ssDNA as well as dsDNA, and DNA-protein complexes. The model opens up large-scale simulations of DNA interacting with a wide range of other (bio)molecules that are available within the Martini framework.
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Cites
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Cited by
Martini 3: A general purpose force field for coarse-grained molecular dynamics
Souza, P. C. T., Alessandri, R., Barnoud, J., Thallmair, S., Faustino, I., Grünewald, F., Patmanidis, I., Abdizadeh, H., Bruininks, B. M. H., Wassenaar, T. A., et al. (2021) · Nature Methods · doi:10.1038/s41592-021-01098-3 · Cited by 1,551
Self-citationCoarse-Grained Protein Models and Their Applications
Kmiecik, S., Gront, D., Kolinski, M., Wieteska, L., Dawid, A. E., & Kolinski, A. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.6b00163 · Cited by 1,071
RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview
Šponer, J., Bussi, G., Krepl, M., Banáš, P., Bottaro, S., Cunha, R. A., Gil-Ley, A., Pinamonti, G., Poblete, S., Jurečka, P., et al. (2018) · Chemical Reviews · doi:10.1021/acs.chemrev.7b00427 · Cited by 599
CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field
Qi, Y., Ingólfsson, H. I., Cheng, X., Lee, J., Marrink, S. J., & Im, W. (2015) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.5b00513 · Cited by 494
Self-citationMartini coarse-grained force field: Extension to RNA
Uusitalo, J. J., Ingólfsson, H. I., Marrink, S. J., & Faustino, I. (2017) · Biophysical Journal · doi:10.1016/j.bpj.2017.05.043 · Cited by 259
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Metadata
- Authors
- Uusitalo, J. J., Ingólfsson, H. I., Akhshi, P., Tieleman, D. P., & Marrink, S. J.
- Venue
- Journal of Chemical Theory and Computation
- Publisher
- American Chemical Society (ACS)
- Published
- 2015-07-23
- Volume
- 11
- Issue
- 8
- Pages
- 3932-3945
- ISSN
- 1549-9618 (ISSN-L)
- 1549-9626
- OpenAlex
- W3169781269
- Cited by
- 320
- References
- 75
- FWCI
- 9.52
- Type
- journal article
- Language
- en
- Open access
- hybrid
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