Martini 3

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Last Updated: Monday, 29 March 2021 18:48

Finally the magic happened: the new version of the Martini forcefield is out. Thanks to the hard work of Paulo Telles de Souza, together with many collaborators, we are happy to share the paper, which just appeared online in Nature Methods. (or try this link for read-only).

Martini3.jpg

Image design: Clarisse Gravina Ricci

Please do not forget to read the supporting information, which is a booklet of 116 pages with all the dirty secrets making this cocktail taste so good ....  Download the new ingredients here!

Realistic membrane shapes

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Last Updated: Friday, 12 March 2021 11:42

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We wrote an opinion paper on the prospects of whole cell modeling, in particular the current efforts in the field to capture realistic membrane shapes.

Curious ? See: Pezeshkian & Marrink, Curr. Opin. Cell Biol., online.

Epithelial plasma membrane

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Last Updated: Friday, 05 March 2021 12:49

Characterization of epithelial plasma membranes with increasing complexity from O'Mara and coworkers, combining lipidomics data with Martini simulations, and highlighting the roles of specific lipids such as plasmalogens, hyrdoxylated sphingholipids, and Forssman lipids. For details: Wilson et al., JCP, 2021. https://doi.org/10.1063/5.0040887

 

Data is available for download here!

Lipid regulated channel

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Last Updated: Wednesday, 03 March 2021 19:07

How a small Martini lipid can shift the conformation, and thereby effect the functioning, of an important membrane protein ... Sounds like a fairy tale ? It is for real ! See Miranda et al., Lipid Regulation of HERG1 Channel, Nature Commun. 2021. https://doi.org/10.1038/s41467-021-21681-8

Go for a Martini at the Bar

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Last Updated: Monday, 22 February 2021 13:35

The power of combining Go-potentials with Martini is nicely demonstrated in this paper from Poma and co-workers, showing how the flexibility and membrane binding mode of an F-Bar protein can be accurately captured: Mahmood et al., Front. Biomol. Sci., 2021. https://doi.org/10.3389/fmolb.2021.619381

Moltemplate

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Last Updated: Thursday, 11 February 2021 15:43

Want to do fancy simulations ? Perhaps Moltemplate is a suitable tool - it can now generate input files which allow you to run Martini simulations for complex systems using LAMMPS.