Pitfalls of MARTINI

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Last Updated: Wednesday, 11 September 2019 04:36

As you hopefully would agree, MARTINI can provide you with beautiful simulations that are undoable with all-atom models. However, it is good to always stay aware of the shortcomings of the model. No free lunch ! In a recent paper we discuss some of these shortcomings that result from the building block principle underlying our model (as well as other CG models). We also discuss potential remedies, providing the rationale for the improvements made in the forthcoming Martini 3.0 version. Enjoy !

Alessandri et al., Pitfalls of the MARTINI model. JCTC, in press. doi.org/10.1021/acs.jctc.9b00473

Protein (had)docking with MARTINI

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Last Updated: Thursday, 03 October 2019 09:06

The group of Bonvin has implemented a scoring function for protein-protein docking, based on the Martini force field, in their popular HADDOCK software package. For details, see: Roel-Touris et al., J Chem Theory Comput. 2019  doi:10.1021/acs.jctc.9b00310

Another paper describes the successful HADdocking of protein-DNA complexes using Martini: Honorato et al., Front. Mol. Biosci., 2019 | https://doi.org/10.3389/fmolb.2019.00102

Toxins destroy membrane

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Last Updated: Tuesday, 18 June 2019 20:27

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Martini simulations from the Hummer group show how toxic peptides form big pores in cholesterol containing membranes.

For details, see: Vogele et al., PNAS 2019, doi.org/10.1073/pnas.1904304116

MERMAID

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Last Updated: Friday, 28 June 2019 14:30

A web server for setting up and running Martini membrane systems has just been launched:

M. Damre, A. Marchetto, A. Giorgetti. MERMAID: dedicated web server to prepare and run coarse-grained membrane protein dynamics. Nucleic Acids Research, gkz416, doi:10.1093/nar/gkz416.

Ceramide binding to VDAC

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Last Updated: Tuesday, 23 April 2019 12:19

VDAC-ceramide.pngStarting as a simple tutorial excercise to demonstrate the power of Martini to study protein-lipid interactions, ending up as a full-blown paper with lots of experimental support and biological relevance ! Read all about the amazing ability of ceramides to bind to voltage dependent anion channels (VDAC) in mitochondrial membranes:

Dadsena et al., Ceramides bind VDAC2 to trigger mitochondrial apoptosis. Nature Commun. 10:1832, 2019. doi:10.1038/s41467-019-09654

Swinger

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Last Updated: Saturday, 20 April 2019 19:56

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Happy Easter with lots of swinging activities .... For inspiration, check out how to convert your CG water beads to real ones on-the-fly !

J. Zavadlav, S.J. Marrink M. Praprotnik, SWINGER: a clustering algorithm for concurrent coupling of atomistic and supramolecular liquids. Interface Focus 9:20180075, 2019. doi.org/10.1098/rsfs.2018.0075