Membrane permeability
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- Last Updated: Monday, 28 March 2022 11:51
Polyply
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- Last Updated: Monday, 10 January 2022 14:02
Generating input files and realistic starting coordinates for complex multi-component simulations is often a major bottleneck, especially for high throughput protocols. To eliminate this bottleneck, we present the polyply software suite that provides 1) a multi-scale graph matching algorithm designed to generate parameters quickly and for arbitrarily complex polymeric topologies, and 2) a generic multi-scale random walk protocol capable of setting up complex systems efficiently and independent of the target force-field or model resolution.
We demonstrate the power of polyply by setting up a number of complex systems, including a liquid-liquid phase separated polymer system inside a lipid vesicle. For details, see Grünewald et al., Nature Commun. 2022.
Massive MuMMI Martinis
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- Last Updated: Wednesday, 05 January 2022 13:08
A huge consortium effort from the Livermore Lab on RAS dynamics, featuring a staggering 120,000 independent Martini simulations, has now been published: Ingolfsson et al., PNAS, 2022.
Impressive work based on the MuMMI (Multiscale Machine-learned Modeling Infrastructure) workflow.
Small molecules
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- Last Updated: Monday, 03 January 2022 12:55
A good start of the new year: Our paper on how to parameterise small molecules with Martini 3 is now published !
You can read about best practices on chosing bead types, handling constraints, and selecting virtual sites for planar compounds, as well as find a large table with best bead types for a wide selection of chemical fragments and numerous validated topologies for small compounds.
Alessandri et al., Adv. Theory & Simul. 2100391. https://doi.org/10.1002/adts.202100391
GPCR-arrestin complex formation
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- Last Updated: Thursday, 23 December 2021 09:02
Martini-based simulations capture the spontaneous binding of beta-arrestin2 to beta2-adrenergic receptor in a similar pose as the crystallographically resolved structure of rhodopsin/arresin-1. Cool !
See the paper from Pluhackova et al.: https://doi.org/10.3389/fcell.2021.807913
The complex formation is found to be dependent on specific lipids, as well as on phosphorylation state. Parameters for phosphorylated serine and threonine in the framework of Martini 2/2P are provided in the SI.
Cell-scale membrane envelope
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- Last Updated: Monday, 20 December 2021 11:55
From the lab of Tajkhorshid: a protocol for setting up simulations of cell-scale membrane envelopes, using Martini.
Paving the way for whole cell simulations !
See Vermaas et al., JCIM, online, for details.