Swarm-CG

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From the Pavan lab: Swarm-CG, a versatile software tool for the automatic iterative parametrization of bonded parameters in coarse-grained models such as Martini.

Details of this promising method have now been published: Empereur-Mot et al., ACS Omega, 2020.

PEGylated proteins

PEGylated-protein.jpgEnhancement of proteins by PEGylation is an active area of research. To gain a better insight into these interactions or even make predictions, we published a protocol on how to simulate PEGylated proteins using the latest iteration of Martini:

F. Grünewald, P.C. Kroon, P.C.T. Souza, S.J. Marrink. Protocol for Simulations of PEGylated Proteins with Martini 3. Structural Genomics: Methods in Molecular Biology 2199:315-335, 2021. reprint

Docking of membrane protein assemblies

Interested in predicting the structure of membrane-associated protein assemblies ? Check out the latest work from the Bonvin group, partially relying on Martini to define the membrane environment: Roel-Touris et al., Nature Commun. 2020.

Peptidoglycan model

A Martini model of bacterial cell wall peptidoglycan is now available, thanks to the nice work of Vaiwala et al. The parameters and other files can be found here.

Death is just the beginning ....

Check out a nice paper from Lucendo et al, in PNAS, showing how TM helix dimerization plays a role in apoptosis. Featuring the Martini 3 beta release, corroborated by atomistic simulations and experimental data.