The DOI matches its Crossref record; 147 of the 151 references it cites were found in a registry or an index.
Martini Coarse-Grained Force Field: Extension to RNA
Open accessAbstract
RNA has an important role not only as the messenger of genetic information but also as a regulator of gene expression. Given its central role in cell biology, there is significant interest in studying the structural and dynamic behavior of RNA in relation to other biomolecules. Coarse-grain molecular dynamics simulations are a key tool to that end. Here, we have extended the coarse-grain Martini force field to include RNA after our recent extension to DNA. In the same way DNA was modeled, the tertiary structure of RNA is constrained using an elastic network. This model, therefore, is not designed for applications involving RNA folding but rather offers a stable RNA structure for studying RNA interactions with other (bio)molecules. The RNA model is compatible with all other Martini models and opens the way to large-scale explicit-solvent molecular dynamics simulations of complex systems involving RNA.
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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-citationComputational Modeling of Realistic Cell Membranes
Marrink, . J., Corradi, V., Souza, P. C. T., Ingólfsson, H. I., Tieleman, D. P., & Sansom, M. S. P. (2019) · Chemical Reviews · doi:10.1021/acs.chemrev.8b00460 · Cited by 715
“196 In addition to lipids, Martini has been extended to the most important classes of biomolecules (proteins, 197,198 carbohydrates, 199 nucleotides 200,201 ), as well as a large variety of polymers 202 and nanoparticles.”
BackgroundSelf-citationRNA 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 606
Two decades of Martini: Better beads, broader scope
Marrink, S. J., Monticelli, L., Melo, M. N., Alessandri, R., Tieleman, D. P., & Souza, P. C. T. (2023) · WIREs Computational Molecular Science · doi:10.1002/wcms.1620 · Cited by 255
Alessandri, R., Souza, P. C. T., Thallmair, S., Melo, M. N., de Vries, A. H., & Marrink, . J. (2019) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.9b00473 · Cited by 231
Metadata
- Authors
- Uusitalo, J. J., Ingólfsson, H. I., Marrink, S. J., & Faustino, I.
- Affiliations
- University of Groningen (NL)
- Corresponding author
- Marrink, Siewert J.
- Venue
- Biophysical Journal
- Publisher
- Elsevier BV
- Published
- 2017-07
- Volume
- 113
- Issue
- 2
- Pages
- 246-256
- ISSN
- 0006-3495 (ISSN-L)
- PMC
- PMC5529176
- OpenAlex
- W2401568999
- Cited by
- 259
- References
- 151
- Citations by year
- 2026: 15 · 2025: 22 · 2024: 31 · 2023: 36 · 2022: 31 · 2021: 34 · 2020: 24 · 2019: 21 · 2018: 20 · 2017: 15
- FWCI
- 8.94
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Biophysical Journal (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (publishedVersion, other-oa)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, other-oa)
- Funders
- Emil Aaltonen Foundation
- Netherlands Scientific Organisation
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
- Keywords
- Martini force field, coarse-grained force field, RNA tertiary structure, elastic networks, RNA-DNA interactions, RNA-protein interactions, explicit solvent molecular dynamics
- MeSH terms
- Elasticity, Humans, Hydrogen Bonding, Ions, Nucleic Acid Conformation, Ribosomes, RNA, Solvents, Water, Thermus thermophilus, RNA Stability, Static Electricity, Molecular Dynamics Simulation, Methanocaldococcus
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