Allosteric pathway unravelled

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Last Updated: Thursday, 21 November 2019 13:52

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Martini-based simulations of a superoxide dismutase protein reveal an allosteric pathway involving an important mutation site. Apart from the biological relevance of this finding, the study is a showcase of how the new Martini 3.0 model is able to capture allosteric coupling in proteins.  For details, see: P.C.T. Souza, S. Thallmair, S.J. Marrink, R. Mera-Adasme. An Allosteric Pathway in SOD1 Unravels the Molecular Mechanism of the G93A ALS-Linked Mutation. J. Phys. Chem. Letters, Just Accepted, 2019. doi.org/10.1021/acs.jpclett.9b02868

Coupling Dry Martini with Lattice Boltzmann

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Last Updated: Friday, 15 November 2019 13:19

Brandner et al. developed a cool new method for the coupling between Dry Martini and Lattice Boltzmann Molecular Dynamics in order to include naturally hydrodynamic interactions in implicit solvent simulations of lipid systems. For details, see: Brandner et al., Scientific Reports 9, 16450 (2019). 

Chemical compound space

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Last Updated: Monday, 28 October 2019 20:25

The team of Bereau published an interesting evaluation of the chemical space that can be represented by the MARTINI bead family. For details, see: Kanakal & Bereau, J. Chem. Phys. 51, 164106 (2019); https://doi.org/10.1063/1.5119101

In memoriam Herman Berendsen

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Last Updated: Wednesday, 09 October 2019 18:31

Herman_Berendsen.jpgHerman Berendsen, one of the founding fathers of molecular modeling, passed away last Monday at the respectable age of 85.

We will miss him, but his legacy is large and will last for generations to come.

MARTINI practical guide

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Last Updated: Thursday, 03 October 2019 16:31

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.

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