Siewert-Jan Marrink
@cg-martini.bsky.social
📤 235
📥 0
📝 39
Martini lover. Shaken, stirred, or self-assembled.
https://cgmartini.nl/
reposted by
Siewert-Jan Marrink
Marieke Westendorp
3 days ago
Instead of a tree, I can offer a snowman! ☃️ Built using bentopy, based on David Naranjo's idea. The input file can be found here:
gist.github.com/ma3ke/723f9c...
.
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Surely someone can make a better Martini X-mas tree?
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3 days ago
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Opportunity: postdoctoral fellowships at the center for Quantitative Cell Biology (QCB), Univ. of Illinois, in close collaboration with our group. Your ticket to become an expert in whole-cell Martini simulations !
qcb.illinois.edu/postdoctoral...
5 days ago
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Martini 3 Building Blocks for Lipid Nanoparticle Design | Journal of Chemical Theory and Computation
pubs.acs.org/doi/full/10....
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Martini 3 Building Blocks for Lipid Nanoparticle Design
Lipid nanoparticles (LNPs) represent a promising platform for advanced drug and gene delivery, yet optimizing these particles for specific cargos and cell targets poses a complex multifaceted challeng...
https://pubs.acs.org/doi/full/10.1021/acs.jctc.5c01207
6 days ago
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reposted by
Siewert-Jan Marrink
Kresten Lindorff-Larsen
11 days ago
The Martini globe. The lipids of the globe are coloured by their continent based on the tectonic plates. The Kingdom of Denmark is coloured dark red. By
@fabianschuhmann.bsky.social
@cg-martini.bsky.social
@weria-lab.bsky.social
et al in
doi.org/10.1021/acs....
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New on the Martini webportal (
cgmartini.nl/docs/contact...
): acknowledgment of all the people who contribute to the development. The list is still growing - if you feel your name should be added please let us know.
9 days ago
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reposted by
Siewert-Jan Marrink
Syma Khalid
22 days ago
Our paper on polymyxin interacting with the E. coli outer membrane is out! Simulations by the very talented
@dheerajprakaash.bsky.social
www.nature.com/articles/s42...
To scale outer membrane protein island simulated at coarse-grained resolution with portions refined at all atom resolution.
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Polymyxins slow down lateral diffusion of proteins and lipopolysaccharide in the E. coli outer membrane - Communications Biology
Multi-scale molecular dynamics simulations reveal that polymyxins form polymyxin-protein aggregates upon associating with the E. coli outer membrane thereby reducing lateral mobility of outer membrane...
https://www.nature.com/articles/s42003-025-09161-x
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reposted by
Siewert-Jan Marrink
Pavol Harar
about 1 month ago
Tomorrow, on 18 Nov, I'll again give a talk at YSS'25. This time, I will present our work on AI-Ready Cryo-Electron Tomography Simulations of the Whole Cell. This is a project I’m especially fond of. I had the idea years ago, and it’s finally taking shape at
@istaresearch.bsky.social
&
@rug.nl
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An optimized contact map for GōMartini 3 enabling conformational changes in protein assemblies
www.biorxiv.org/content/10.1...
about 1 month ago
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CCD2MD: A Suite of Packages for Preparing Co-Folded Outputs for Molecular Dynamics Simulations | Journal of Chemical Information and Modeling
pubs.acs.org/doi/full/10....
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CCD2MD: A Suite of Packages for Preparing Co-Folded Outputs for Molecular Dynamics Simulations
Protein–lipid interactions play a crucial role in the stability and function of membrane proteins. While experimental approaches to characterize these interactions in a native-like membrane environment can be challenging, computational techniques offer a powerful alternative for identifying and analyzing potential binding sites. Recent advances in cofolding methods now enable the prediction of holo protein structures, capturing conformational changes that may occur upon lipid binding and thereby improving the accuracy of binding site characterization. However, the outputs from these methods often require postprocessing to ensure compatibility with widely used molecular dynamics force fields. In this work, we introduce CCD2MD, a modular toolkit designed to convert cofolding outputs into simulation-ready systems for GROMACS. CCD2MD supports both atomistic and coarse-grained representations with or without membrane embedding. While CCD2MD is exemplified here with protein–lipid systems, its modular design allows for straightforward adaptation to other cofolded biomolecular assemblies, incorporating complexes with nucleic acids, small molecules, carbohydrates, or metal ions, thereby enabling a variety of simulation setups across multiple scales.
https://pubs.acs.org/doi/full/10.1021/acs.jcim.5c02066
about 2 months ago
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reposted by
Siewert-Jan Marrink
Maksim Kalutskii
2 months 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
2 months 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
2 months ago
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Coarse-Grained Martini 3 Model for Collagen Fibrils: Biophysical Journal
www.cell.com/biophysj/ful...
3 months 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
3 months ago
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reposted by
Siewert-Jan Marrink
Gene Chong
3 months 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
3 months 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
3 months 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
4 months ago
0
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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/...
4 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...
4 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
4 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
5 months ago
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reposted by
Siewert-Jan Marrink
5 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
6 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
6 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
6 months ago
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reposted by
Siewert-Jan Marrink
Matthieu Chavent
7 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
7 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
7 months ago
0
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reposted by
Siewert-Jan Marrink
Mathieu Linares
7 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.
7 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...
8 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
8 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.
8 months ago
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reposted by
Siewert-Jan Marrink
Weria Pezeshkian
8 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
9 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
9 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
9 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
9 months ago
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reposted by
Siewert-Jan Marrink
Manuel N. Melo at ITQB NOVA
9 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
10 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
10 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
10 months ago
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reposted by
Siewert-Jan Marrink
BioExcel CoE
10 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
11 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
11 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
11 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
11 months ago
0
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