Siewert-Jan Marrink
@cg-martini.bsky.social
📤 228
📥 0
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Martini lover. Shaken, stirred, or self-assembled.
https://cgmartini.nl/
reposted by
Siewert-Jan Marrink
Maksim Kalutskii
12 days ago
📜 New preprint! We developed PoGö, an algorithm to optimize the essential dynamics of GöMartini proteins based on all-atom simulations:
www.biorxiv.org/content/10.1...
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reposted by
Siewert-Jan Marrink
Weria Pezeshkian
12 days ago
the Martini Pumpkin by my PhD student Isabell Lindahl. Too much fat though! TS2CG, Martini3, Martini
@cg-martini.bsky.social
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Allosteric pathway connects Zn(II) loss from SOD1 to known pathogenic ...
www.sciencedirect.com/science/arti...
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Allosteric pathway connects Zn(II) loss from SOD1 to known pathogenic mechanisms
Cu,Zn superoxide dismutase (SOD1) is one of the proteins with mutations linked to hereditary forms of the amyotrophic lateral sclerosis neurodegenerat…
https://www.sciencedirect.com/science/article/pii/S0141813025089068
17 days ago
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Coarse-Grained Martini 3 Model for Collagen Fibrils: Biophysical Journal
www.cell.com/biophysj/ful...
29 days ago
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Nobel Prize for Martini ! Terrific news ! Well deserved of course. Oh shoot .... Martinis ...
add a skeleton here at some point
about 1 month ago
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reposted by
Siewert-Jan Marrink
Gene Chong
about 1 month ago
Are the lipids associated with static protein structures there as long-lived ligands or an effect of preferential solvation? This computational-experimental framework shows the way!
#lipidtime
#compchem
www.nature.com/articles/s41...
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Molecular basis for the regulation of membrane proteins through preferential lipid solvation - Nature Chemical Biology
Static protein structures can capture the association of lipids, but it is unclear whether the association is due to lipids acting as long-lived ligands or the solvation of preferred lipids around the protein. A computational-experimental framework has now shown that for the protein CLC-ec1, it is the change in lipid solvation energies that drives dimerization, with preferred lipids around the protein modulating this driving force.
https://www.nature.com/articles/s41589-025-02032-w?utm_source=bluesky&utm_medium=social&utm_campaign=nchembio
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How does Mycoplasma pneumoniae scavenge lipids from its host membranes? | Science Advances
www.science.org/doi/full/10....
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How does Mycoplasma pneumoniae scavenge lipids from its host membranes?
P116 is an adaptive, all-in-one lipid acquisition machinery fit for any host environment.
https://www.science.org/doi/full/10.1126/sciadv.ady4746?af=R
about 1 month ago
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Cool paper from our former guest student Laura, combining fancy experiments with titratable Martini simulations on supramolecular self-assembled systems as versatile platforms for bio-engineering. Advanced Science,
doi.org/10.1002/advs...
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Peptide Electrostatic Modulation Directs Human Neural Cell Fate
This study explores the effect of charge on the bioactivity of peptide-based supramolecular materials. The design of a peptide library with varying charges that self-assemble into supramolecular fibe....
https://doi.org/10.1002/advs.202507946
about 1 month ago
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Martini 3 Coarse-Grained Models for Carbon Nanomaterials | Journal of Chemical Theory and Computation
pubs.acs.org/doi/full/10....
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Martini 3 Coarse-Grained Models for Carbon Nanomaterials
The Martini model is a coarse-grained force field allowing simulations of biomolecular systems as well as a range of materials including different types of nanomaterials of technological interest. Recently, a new version of the force field (version 3) has been released that includes new parameters for lipids, proteins, carbohydrates, and a number of small molecules, but not yet carbon nanomaterials. Here, we present new Martini models for three major types of carbon nanomaterials: fullerene, carbon nanotubes, and graphene. The new models were parametrized within the Martini 3 framework, and reproduce semiquantitatively a range of properties for each material. In particular, the model of fullerene yields excellent solid-state properties and good properties in solution, including correct trends in partitioning between different solvents and realistic translocation across lipid membranes. The models of carbon nanotubes reproduce the atomistic behavior of nanotube porins spanning lipid bilayers. The model of graphene reproduces structural and elastic properties, as well as trends in experimental adsorption enthalpies of organic molecules. All new models can be used in large-scale simulations to study the interaction with the wide variety of molecules already available in the Martini 3 force field, including biomolecular and synthetic systems.
https://pubs.acs.org/doi/full/10.1021/acs.jctc.5c00923
2 months ago
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Martini on top of the world ! TS2CG as a Membrane Builder | Journal of Chemical Theory and Computation
pubs.acs.org/doi/10.1021/...
2 months ago
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Dynamics and lipid membrane coupling of the RAS-RAF complex revealed via multiscale simulations: Biophysical Journal
www.cell.com/biophysj/ful...
3 months ago
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Cool simulations from my former PhD student Petteri Vainikka now published: "Molecular Dynamics Simulation of Fatty Acid Extraction Using a Type V Deep Eutectic Solvent with Tunable Hydrophobicity" | The Journal of Physical Chemistry B
pubs.acs.org/doi/full/10....
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Molecular Dynamics Simulation of Fatty Acid Extraction Using a Type V Deep Eutectic Solvent with Tunable Hydrophobicity
Deep eutectic solvents (DESs) are often promoted as a more environmentally friendly alternative for ionic liquids and other ionic solvents. Like ionic liquids, DESs can be designed for specific tasks ...
https://pubs.acs.org/doi/full/10.1021/acs.jpcb.4c08261
3 months ago
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A true community effort ! The Martini 3 Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior | ACS Central Science
pubs.acs.org/doi/10.1021/...
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https://pubs.acs.org/doi/10.1021/acscentsci.5c00755
3 months ago
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reposted by
Siewert-Jan Marrink
3 months ago
It is yet another story through the optics of coarse grained molecular dynamics simulations (using the Martini3
@cg-martini.bsky.social
model) about the ATP synthase and its favorite lipid companion: the four-tailed lipid cardiolipin.
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reposted by
Siewert-Jan Marrink
Adrien Schahl
4 months ago
@cg-martini.bsky.social
presenting the work of his lab about CG modelling of whole cell, notably with publications from
@janstevens.bsky.social
#EBSA2025
🤩
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reposted by
Siewert-Jan Marrink
Chelsea Brown
4 months ago
What better way to use my first proper post than to share my first big piece of post-doctoral work with
@cg-martini.bsky.social
! Here, we used integrative modelling to build and simulate a mitochondrial cristae. Find the paper here (
rdcu.be/eujAC
) or see below for a quick overview 👇
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A FEW LASTS SPOTS AVAILABLE, REGISTER NOW !!
add a skeleton here at some point
5 months ago
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reposted by
Siewert-Jan Marrink
Matthieu Chavent
5 months ago
Very happy to release AutoMartiniM3 for Martini3 to automatize CG modelling of small molecules and fragments. Great work from M Szczuka in my lab in collab with
@pauloctsouza.bsky.social
and
@tbereau.bsky.social
teams! Give it a try:
github.com/Martini-Forc...
poke
@cg-martini.bsky.social
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Registration deadline June 15 approaching ....
add a skeleton here at some point
5 months ago
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MA(R/S)TINI 3: An Enhanced Coarse-Grained Force Field for Accurate Modeling of Cyclic Peptide Self-Assembly and Membrane Interactions | Journal of Chemical Theory and Computation
pubs.acs.org/doi/full/10....
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https://pubs.acs.org/doi/full/10.1021/acs.jctc.5c00126
5 months ago
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reposted by
Siewert-Jan Marrink
Mathieu Linares
5 months ago
Interactive visualization of
@cg-martini.bsky.social
bacterial cell with
@viamd.bsky.social
.
#compchem
@gromacs.bsky.social
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Martini workshop registration now open !!!! See
cgmartini.nl
for details and how to apply. Looking forward to seeing you in Groningen, Aug 11-15th.
5 months ago
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PFAS surfactants self-assemble into vesicles. Exciting results based on Martini simulations from Bei Yan, highlighted in Nature:
www.nature.com/articles/d41...
6 months ago
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GoGoGoGoGoGoGoMartini3 now finally published !
www.nature.com/articles/s41...
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GōMartini 3: From large conformational changes in proteins to environmental bias corrections - Nature Communications
This work presents GōMartini 3, an improved coarse-grained protein model combining physics- and structure-based approaches. It boosts computational efficiency and accuracy for structured soluble and m...
https://www.nature.com/articles/s41467-025-58719-0
6 months ago
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Pre-announcement: MARTINI tutorial workshop, August 11-15th 2025 in Groningen, The Netherlands !! Learn basic and advanced Martini from the cocktail masters themselves. Registration will open soon.
6 months ago
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reposted by
Siewert-Jan Marrink
Weria Pezeshkian
7 months ago
New preprint: TS2CG version 2, building and simulating membranes with any shape and lateral organisation. We got Martini Globe, Martini Möbius strip and again mitochondrion.
www.biorxiv.org/content/10.1...
@cg-martini.bsky.social
@janstevens.bsky.social
@fabianschuhmann.bsky.social
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ART-SM: Boosting Fragment-Based Backmapping by Machine Learning | Journal of Chemical Theory and Computation
pubs.acs.org/doi/10.1021/...
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ART-SM: Boosting Fragment-Based Backmapping by Machine Learning
In sequential multiscale molecular dynamics simulations, which advantageously combine the increased sampling and dynamics at coarse-grained resolution with the higher accuracy of atomistic simulations...
https://pubs.acs.org/doi/10.1021/acs.jctc.5c00189
7 months ago
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CGsmiles: A Versatile Line Notation for Molecular Representations across Multiple Resolutions | Journal of Chemical Information and Modeling
pubs.acs.org/doi/10.1021/...
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CGsmiles: A Versatile Line Notation for Molecular Representations across Multiple Resolutions
Coarse-grained (CG) models simplify molecular representations by grouping multiple atoms into effective particles, enabling faster simulations and reducing the chemical compound space compared to atom...
https://pubs.acs.org/doi/10.1021/acs.jcim.5c00064
7 months ago
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MartiniGlass: a Tool for Enabling Visualization of Coarse-Grained Martini Topologies | Journal of Chemical Information and Modeling
pubs.acs.org/doi/10.1021/...
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MartiniGlass: a Tool for Enabling Visualization of Coarse-Grained Martini Topologies
As molecular modeling gains ever more prominence in understanding cellular processes, high quality visualization of models and dynamics has never been more important. Naturally, much molecular visuali...
https://pubs.acs.org/doi/10.1021/acs.jcim.4c02277
8 months ago
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Martini 3 - IDP is out! Improved parameters for disordered proteins, great work from Liguo Wang:
www.nature.com/articles/s41...
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Martini3-IDP: improved Martini 3 force field for disordered proteins - Nature Communications
Here, the authors introduce Martini3-IDP, a refined model for disordered proteins that addresses prior over-compact structures. Validated across diverse systems, it captures IDP interactions and biomo...
https://www.nature.com/articles/s41467-025-58199-2
8 months ago
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reposted by
Siewert-Jan Marrink
Manuel N. Melo at ITQB NOVA
8 months ago
Cool new AMP pore structures and a membrane activity dependent on lipid shape, in our new paper by
@marmakow.bsky.social
! (Using the old-but-gold Martini 2 model from
@cg-martini.bsky.social
)
#compchem
#compbiophys
#compbiol
🖥️🧪
pubs.acs.org/doi/full/10....
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Lipid Shape as a Membrane Activity Modulator of a Fusogenic Antimicrobial Peptide
An intriguing feature of many bacterial membranes is their prevalence of non-bilayer-forming lipids, such as the cone-shaped phosphatidylethanolamines and cardiolipins. Many membrane-active antimicrob...
https://pubs.acs.org/doi/full/10.1021/acs.jcim.4c02020
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Simulations of a nano-pore inside a hybrid lipid-block copolymer membrane:
doi.org/10.1002/adma...
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Nanopore‐Functionalized Hybrid Lipid‐Block Copolymer Membranes Allow Efficient Single‐Molecule Sampling and Stable Sensing of Human Serum
Biological nanopores are highly promising tools for single-molecule biosensors, but the fragile supporting lipid membranes is a major bottleneck. An alternative hybrid membrane is presented, comprisi...
https://doi.org/10.1002/adma.202418462
8 months ago
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Post-doc position on whole-cell modelling available at the Quantitative Cell Biology Center (Univ. of Illinois) ! Your chance to simulate entire cells with Martini and to integrate Martini with lattice microbes, in collaboration with my group. See
qcb.illinois.edu/members/post...
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QCB Postdoctoral Fellowships
Postdoc positions with the Center for Quantitative Cell Biology at University of Illinois Urbana-Champaign.
https://qcb.illinois.edu/members/postdoctoral-fellowships
8 months ago
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Cool paper from the Risselada group, based on Evo-MD: Toward the Evolutionary Optimisation of Small Molecules Within Coarse-Grained Simulations: Training Molecules to Hide Behind Lipid Head Groups | The Journal of Physical Chemistry B
pubs.acs.org/doi/full/10....
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Toward the Evolutionary Optimisation of Small Molecules Within Coarse-Grained Simulations: Training Molecules to Hide Behind Lipid Head Groups
Exploring the vast chemical space of small molecules poses a significant challenge. We develop a new strategy to efficiently explore this space using coarse-grained toy-like molecules utilizing the Martini3 force field and graph representations. This yields initial proof-of-concept results for the approach enabling the identification of optimal molecules with specific properties targeting lipid bilayers. By leveraging genetic algorithms and coarse-grained molecular dynamics simulations, we demonstrate the potential of our method in designing simple, linear molecules. Our findings show a good convergence toward molecules with weak amphiphilic properties, resembling known (general anesthetic) molecules. While this study demonstrates the feasibility of our method, further refinement is needed to fully realize its potential and explore more complex molecular topologies. Nevertheless, these encouraging results suggest a new path for future research in small molecule discovery and design without relying on extensive data sets.
https://pubs.acs.org/doi/full/10.1021/acs.jpcb.4c08200
8 months ago
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reposted by
Siewert-Jan Marrink
BioExcel CoE
9 months ago
The ability to simulate whole cells will take biological research to a new level 🦠🔬📈 Join us on 18 March 2025, 15:00 CET to hear Siewert-Jan Marrink present progress on simulating whole cells with the Martini force field Registration ➡️bit.ly/3QxQWSC
@cg-martini.bsky.social
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reposted by
Siewert-Jan Marrink
Manuel N. Melo at ITQB NOVA
9 months ago
More VDAC shenanigans, now in interaction with Hexokinase I, in another great collaborative work with
@holthuislab.bsky.social
and
@cg-martini.bsky.social
!
www.nature.com/articles/s42...
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reposted by
Siewert-Jan Marrink
Niek van Hilten
9 months ago
Our paper is now out in
@elife.bsky.social
! We performed
@cg-martini.bsky.social
MD simulations to capture >700 lipid scrambling events in 27 TMEM16 structures to systematically study their lipid scrambling rates and mechanisms. 📃
doi.org/10.7554/eLife.105111.1
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Excellent review including a comprehensive section on what Martini can do in this field: "Computational Methods for Modeling Lipid-Mediated Active Pharmaceutical Ingredient Delivery | Molecular Pharmaceutics"
pubs.acs.org/doi/10.1021/...
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Computational Methods for Modeling Lipid-Mediated Active Pharmaceutical Ingredient Delivery
Lipid-mediated delivery of active pharmaceutical ingredients (API) opened new possibilities in advanced therapies. By encapsulating an API into a lipid nanocarrier (LNC), one can safely deliver APIs n...
https://pubs.acs.org/doi/10.1021/acs.molpharmaceut.4c00744
9 months ago
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Free Energy, Rates, and Mechanism of Transmembrane Dimerization in Lipid Bilayers from Dynamically Unbiased Molecular Dynamics Simulations | The Journal of Physical Chemistry B
pubs.acs.org/doi/10.1021/...
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Free Energy, Rates, and Mechanism of Transmembrane Dimerization in Lipid Bilayers from Dynamically Unbiased Molecular Dynamics Simulations
The assembly of proteins in membranes plays a key role in many crucial cellular pathways. Despite their importance, characterizing transmembrane assembly remains challenging for experiments and simula...
https://pubs.acs.org/doi/10.1021/acs.jpcb.4c05242
9 months ago
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Confinement Induces Morphological and Topological Transitions in Multivesicles | ACS Nano
pubs.acs.org/doi/abs/10.1...
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Confinement Induces Morphological and Topological Transitions in Multivesicles
The study of self-assembly in confined spaces has gained significant attention among amphiphilic superstructures and colloidal design. The additional complexity introduced by interactions between cont...
https://pubs.acs.org/doi/abs/10.1021/acsnano.4c14171
10 months ago
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reposted by
Siewert-Jan Marrink
Syma Khalid
10 months ago
So seems like the group is on a roll this month! Here’s our latest work on parametrising coarse-grained models of sugars (disaccharides) by Astrid Brandner & in collaboration with Iain Smith,
@pauloctsouza.bsky.social
and
@cg-martini.bsky.social
pubs.acs.org/doi/10.1021/...
#glycotime
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Systematic Approach to Parametrization of Disaccharides for the Martini 3 Coarse-Grained Force Field
Sugars are ubiquitous in biology; they occur in all kingdoms of life. Despite their prevalence, they have often been somewhat neglected in studies of structure–dynamics–function relationships of macro...
https://pubs.acs.org/doi/10.1021/acs.jcim.4c01874
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Validation of a Coarse-Grained Martini 3 Model for Molecular Oxygen | Journal of Chemical Theory and Computation
pubs.acs.org/doi/10.1021/...
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Validation of a Coarse-Grained Martini 3 Model for Molecular Oxygen
Molecular oxygen (O2) is essential for life, and continuous effort has been made to understand its pathways in cellular respiration with all-atom (AA) molecular dynamics (MD) simulations of, e.g., mem...
https://pubs.acs.org/doi/10.1021/acs.jctc.4c01348
10 months ago
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Happy ending (of the year): the release of our preprint, "The Martini 3 Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior", now available on @ChemRxiv. 👉 Read the full preprint here:
chemrxiv.org/engage/chemr...
and get the parameters here:
github.com/Martini-Forc...
11 months ago
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Benchmarking a dual-scale hybrid simulation framework for small globul...
www.sciencedirect.com/science/arti...
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Benchmarking a dual-scale hybrid simulation framework for small globular proteins combining the CHARMM36 and Martini2 models
Multi-scale models in which varying resolutions are considered in a single molecular dynamics simulation setup are gaining importance in integrative m…
https://www.sciencedirect.com/science/article/pii/S1093326324002262
11 months ago
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G-Protein-Coupled Receptor Surface Creates a Favorable Pathway for Membrane Permeation of Drug Molecules | The Journal of Physical Chemistry Letters
pubs.acs.org/doi/10.1021/...
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G-Protein-Coupled Receptor Surface Creates a Favorable Pathway for Membrane Permeation of Drug Molecules
G-protein-coupled receptors (GPCRs) play a crucial role in modulating physiological responses and serve as the main drug target. Specifically, salmeterol and salbutamol, which are used for the treatme...
https://pubs.acs.org/doi/10.1021/acs.jpclett.4c02875
11 months ago
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Multiple-Basin Gō-Martini for Investigating Conformational Transitions and Environmental Interactions of Proteins
www.biorxiv.org/content/10.1...
11 months ago
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Martignac: Computational Workflows for Reproducible, Traceable, and Composable Coarse-Grained Martini Simulations | Journal of Chemical Information and Modeling
pubs.acs.org/doi/10.1021/...
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Martignac: Computational Workflows for Reproducible, Traceable, and Composable Coarse-Grained Martini Simulations
Despite their wide use and far-reaching implications, molecular dynamics (MD) simulations suffer from a lack of both traceability and reproducibility. We introduce Martignac: computational workflows f...
https://pubs.acs.org/doi/10.1021/acs.jcim.4c01754
11 months ago
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