The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations
Open accessAbstract
We present an improved and extended version of our coarse grained lipid model. The new version, coined the MARTINI force field, is parametrized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical compounds. To reproduce the free energies of these chemical building blocks, the number of possible interaction levels of the coarse-grained sites has increased compared to those of the previous model. Application of the new model to lipid bilayers shows an improved behavior in terms of the stress profile across the bilayer and the tendency to form pores. An extension of the force field now also allows the simulation of planar (ring) compounds, including sterols. Application to a bilayer/cholesterol system at various concentrations shows the typical cholesterol condensation effect similar to that observed in all atom representations.
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Cites
VMD: visual molecular dynamics
Humphrey, W., Dalke, A., & Schulten, K. (1996) · Journal of Molecular Graphics · doi:10.1016/0263-7855(96)00018-5 · Cited by 66,952
CRC Handbook of Chemistry and Physics
(2014) · doi:10.1201/b17118 · Cited by 57,706
Coarse Grained Model for Semiquantitative Lipid Simulations
Marrink, S. J., de Vries, A. H., & Mark, A. E. (2004) · The Journal of Physical Chemistry B · doi:10.1021/jp036508g · Cited by 2,257
Molecular Basis for Dimethylsulfoxide (DMSO) Action on Lipid Membranes
Notman, R., Noro, M., O'Malley, B., & Anwar, J. (2006) · Journal of the American Chemical Society · doi:10.1021/ja063363t · Cited by 447
Lipids Out of Equilibrium: Energetics of Desorption and Pore Mediated Flip-Flop
Tieleman, D. P., & Marrink, S.-J. (2006) · Journal of the American Chemical Society · doi:10.1021/ja0624321 · Cited by 230
Self-citation
Cited by
Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015) · SoftwareX · doi:10.1016/j.softx.2015.06.001 · Cited by 27,190
Computer Simulation of Liquids
Allen, M. P., & Tildesley, D. J. (2017) · doi:10.1093/oso/9780198803195.001.0001 · Cited by 20,945
Oxidized arachidonic and adrenic PEs navigate cells to ferroptosis
Kagan, V. E., Mao, G., Qu, F., Angeli, J. P. F., Doll, S., Croix, C. S., Dar, H. H., Liu, B., Tyurin, V. A., Ritov, V. B., et al. (2017) · Nature Chemical Biology · doi:10.1038/nchembio.2238 · Cited by 3,029
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-citation‘Improved parameters for the Martini coarse-grained protein force field’
de Jong, D. H., Singh, G., Bennett, W. F. D., Arnarez, C., Wassenaar, T. A., Schäfer, L. V., Periole, X., Tieleman, D. P., & Marrink, S. J. (2013) · Journal of Chemical Theory and Computation · doi:10.1021/ct300646g · Cited by 1,486
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Metadata
- Authors
- Marrink, S. J., Risselada, H. J., Yefimov, S., Tieleman, D. P., & de Vries, A. H.
- Venue
- The Journal of Physical Chemistry B
- Publisher
- American Chemical Society (ACS)
- Published
- 2007-06-15
- Volume
- 111
- Issue
- 27
- Pages
- 7812-7824
- ISSN
- 1520-5207 (ISSN-L)
- 1520-6106
- OpenAlex
- W2119267663
- Cited by
- 5,562
- References
- 5
- FWCI
- 36.28
- Type
- journal article
- Language
- en
- Open access
- green
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