MARTINI practical guide

If you would like some guidance on how to setup complex MARTINI simulations, the tips and tricks behhind the scene, have a look at this book chapter: Bruininks et al., "A Practical View of the Martini Force Field", Biomolecular Simulations, 105-127, 2019. pdf-reprint.

Post-doctoral Position in: De novo Nanopore Design

A postdoctoral position is available for a joint project between the laboratories of Prof. G Maglia and Prof. SJ Marrink at the University of Groningen, the Netherlands.
Biological nanopores are an exciting new class of biosensors, which found practical application in single-molecule DNA sequencing and single-molecule analysis. This project aims at the challenging task of de novo design of new nanopores. The prospective candidate will contribute to this aim with state-of-the-art molecular dynamics simulations and related tools, and work closely together with experimental colleagues. For more information and how to apply, see (full document).

Pitfalls of MARTINI

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

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., 

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

pore-pnas.png

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

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.