RNA extension in Martini

rna Figure7

Now we can also simulate RNA systems with Martini. Check out our publication in Biophysical Journal. Single strand and double strand RNA molecules can now be simulated together with other biomolecules. You can download the parameters here.

 J.J. Uusitalo, H.I. Ingólfsson, S.J. Marrink, I. Faustino. Martini coarse-grained force field: extension to RNA. Biophys. J., online, 2017. DOI: http://dx.doi.org/10.1016/j.bpj.2017.05.043

Martinizing VISM

Check out this cool paper,  pushing the Variational Implicit Solvent Method (VISM) to larger scale applications by combining it with solute Hamiltonians adapted from the MARTINI framework: 
C.G. Ricci, B. Li, L.T. Cheng, J. Dzubiella, J.A. McCammon. JPCB, 2017. online

MD simulations reveal chaos in electron transport

Using Martini, we were able to simulate the spontaneous binding and unbinding of electron carriers to photosystem II, one of the key protein complexes in photosynthesis. For more details, please see the full paper:

F.J. van Eerden, M.N. Melo, P.W.J.M. Frederix, X. Periole, S.J. Marrink. Exchange pathways of plastoquinone and plastoquinol in the photosystem II complex. Nature Commun. 8:15214, 2017. http://rdcu.be/rU3i

or check out the various press releases (including a cool movie):

cover art PLQ

Announcing the 2017 Martini Coarse-Graining Workshop

Are you impressed by the interesting science done by using the Martini coarse-grained model, and do you want to hear from the developers about the philosophy, background, current, and future developments of Martini? Moreover, do you want to practice coarse-graining skills under the guidance of Martini experts? The Martini summerschool is the place for you!

Registration closed

Read more: Announcing the 2017 Martini Coarse-Graining Workshop

DNA nanopores

DNA origami pore in bilayer

A nice application of the Martini DNA model in assessing properties of membrane spanning DNA-based nanopores:

Maingi et al., Nature Comm. 14784 (2017). doi:10.1038/ncomms14784

Intoxicated MscL (too many Martinis ?)

MscL opened in silico

Membrane mediated effects of alcohols on MscL function revealed using
high throughput, 600+, Martini simulations.

M.N. Melo, C. Arnarez, H. Sikkema, N. Kumar, M. Walko, H.J.C. Berendsen, A. Kocer, S.J. Marrink, H.I. Ingólfsson. High-throughput simulations reveal membrane-mediated effects of alcohols on MscL gating. JACS, 139:2664–2671, 2017. open access