LATEST NEWS
In memoriam Herman Berendsen
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- Last Updated: Wednesday, 09 October 2019 18:31
Herman 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.
Post-doctoral Position in: De novo Nanopore Design
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- Last Updated: Thursday, 12 September 2019 22:47
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
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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.,
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