LATEST NEWS

GPCRs in action

A topical review on CG simulations of GPCRs, featuring many Martini-based works, is now online at ACS Chemical Reviews:

X. Periole. Interplay of G Protein-Coupled Receptors with the Membrane: Insights from Supra-Atomic Coarse Grain Molecular Dynamics Simulations. Chem Rev. Article ASAP. doi:10.1021/acs.chemrev.6b00344

Replica exchange umbrella sampling

Another paper from the Sansom lab showing how protein-protein and protein-lipid PMFs with MARTINI can be efficiently obtained using replica-exchange umbrella sampling:

J. Domanski, G. Hedger, R.B. Best, P.J. Stansfeld, and M.S.P. Sansom. Convergence and sampling in determining free energy landscapes for membrane protein association. J. Phys. Chem. B, Just Accepted. doi:10.1021/acs.jpcb.6b08445

Complexity of the photosynthetic machinery captured by Martini

We proudly present the most recent work of F. J. van Eerden a PhD student in our lab, soon to graduate.

F.J. van Eerden, T. van den Berg, P.W.J.M. Frederix, D.H. de Jong, X. Periole, S.J. Marrink. Molecular dynamics of photosystem II embedded in the thylakoid membrane. JPCB,2016, Accepted Manuscript. doi:10.1021/acs.jpcb.6b06865

toc PSII

Martini metadynamics

Check out this paper, a nice example of how metadynamics can be combined with Martini for efficient sampling of protein-protein binding free energies:

, , and Conformational changes in the epidermal growth factor receptor: role of the transmembrane domain investigated by Coarse-Grained metadynamics free energy calculations.  J. Am. Chem. Soc., Just Accepted. doi:10.1021/jacs.6b05602

Protein side chains

The team of Prof. Vogel has developed a fix to prevent side chains from flipping to the wrong side of beta strands. Soon to be implemented in martinize. For details, see:

F.A. Herzog, L. Braun, I. Schoen, V. Vogel. Improved side chain dynamics in Martini simulations of protein-lipid interfaces. JCTC, online. doi:10.1021/acs.jctc.6b00122