Relevance of lipid complexity

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Last Updated: Thursday, 14 January 2021 15:43

Check out this nice paper on modeling E.coli lipid membranes at multiple levels of compositional complexity, showing that the presence of many different lipid types gives these membranes their distinct properties. And, demonstrating excellent performance of the preliminary Martini 3 lipids !

Pluhackova & Horner, "Native-like membrane models of E. coli polar lipid extract shed light on the importance of lipid composition complexity", BMC Biology, 2021. online.

Nucleotide cofactors & metabolites

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Last Updated: Friday, 08 January 2021 15:49

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All these small but essential molecules Martinized especially for you by the Melo team. Check it out: Sousa et al., JCIM, 2021

The paper describes Martini topologies for key metabolites and cofactors (FAD, FMN, riboflavin, NAD, NADP, ATP, ADP, AMP, and thiamine pyrophosphate) in different oxidation and protonation states as well as smaller molecules derived from them (among others, nicotinamide, adenosine, adenine, ribose, thiamine, and lumiflavin), summing up a total of 79 different molecules.

The topologies are available for download here!

Martini Perspective in Materials Science

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Last Updated: Wednesday, 16 December 2020 11:22

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Martini applications in material science is a booming field.

We summarized the progress in this field, and provided a critical outlook, in a perspective paper which is now available in the arXiv.

Just blow it up ...

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Last Updated: Tuesday, 15 December 2020 11:12

exploding tree

 

If you feel bored during the Xmas break, or simply want to get rid of your Martini frustrations, please experiment with exploding Martini-bead snowmen, Santaclaus, or other stuff you'ld like to see blasted (bunnies !).

Who says Martini is too sticky ?

We would like to wish you all a merry Christmas and a happy new year, please stay healthy and may you all have a blast ...

Swarm-CG

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Last Updated: Thursday, 10 December 2020 11:40

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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

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Last Updated: Monday, 30 November 2020 09:14

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