Plasma membrane

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Last Updated: Thursday, 11 June 2015 16:18

plasma membrane TOCPlasma membrane model composed of 60+ lipid types

H.I. Ingólfsson, M.N. Melo, F.J. van Eerden, C. Arnarez, C.A. López, T.A. Wassenaar, X. Periole, A.H. De Vries, D.P. Tieleman, S.J. Marrink. Lipid organization of the plasma membrane. JACS, 136:14554-14559, 2014. doi: 10.1021/ja507832e open access

Example membranes and parameter files are provided here

Martini in Science

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Last Updated: Saturday, 16 August 2014 09:20

Publication featuring the Martini force field in Science:

"Polyunsaturated phospholipids facilitate membrane deformation and fission by endocytic proteins"

Pinot et al.,  Science 2014, 345:693-697

Martini DNA beta

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Last Updated: Wednesday, 22 July 2015 10:03

A beta version of Martini parameters for both single-stranded and double-stranded DNA are available for testing.

The parameters are still under development and currently we recommend testing them in sytems that contain either stable double-stranded DNAs or short single-stranded DNAs.
 

Read more: Martini DNA beta

AdResSing MARTINI

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Last Updated: Sunday, 20 July 2014 06:38

adressGood news for multiscalers: Adaptive resolution simulation with MARTINI

J. Zavadlav, M. N. Melo, S.J. Marrink, M. Praprotnik.
Adaptive resolution simulation of an atomistic protein in MARTINI water.
J. Chem. Phys., 140:054114, 2014. open access

Going backward

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Last Updated: Wednesday, 19 March 2014 09:37

backwardNew tool for fast backmapping

T.A. Wassenaar, K. Pluhackova, R. Böckmann, S.J. Marrink, D.P. Tieleman.
Going backward: A flexible geometric approach to reverse transformation from coarse grained to atomistic models.
JCTC, 10:676-690, 2014.

For details, read the paper, and/or try out the tool yourself

Coarse grain protein-protein interactions

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Last Updated: Sunday, 01 December 2013 13:39

Review online: "Coarse grain modelling of protein–protein interactions"

M. Baaden, S.J. Marrink. Curr. Opin. Struct. Biol., 23:878:886, 2013. open access