‪Siewert J. Marrink

This study shows that actin and AnkJ reciprocally regulate the catalytic activity of Ceg14 by remodeling its catalytic center.

This study evaluates coarse-grained funnel metadynamics for modeling ligand binding at the tubulin colchicine site, showing improved statistical convergence and reasonable accuracy compared to all-atom simulations.

The paper shows that lipid asymmetry drives pore formation in membranes, which function as self-resealing scramblases to restore balance.

This paper parameterizes 186 common metabolites for the Martini 3 force field to enable realistic simulations of metabolite interactions in biological systems.

The paper optimizes the contact map in GoMartini 3 by integrating dynamic contact information from AA-MD simulations, improving conformational sampling and representation in biomolecular assemblies.

The paper shows that protein agglomerates in E. coli regulate cytoplasmic rheology, with diffusion inversely correlating with amino acid metabolism protein abundance.

The paper investigates oxygen partitioning into biomolecular condensates and finds that oxygen concentration varies with protein density and chain length.

The paper introduces a web portal for the Martini Force Field Initiative to facilitate open collaboration and resource management in biomolecular simulations.

The paper updates the MAD web server with new tools and an enhanced database for building and simulating coarse-grained polymer models using the Martini force field.

This study compares the mechanical stability of antibody and nanobody interactions with SARS-CoV-2 variants using nanomechanical simulations.

This study shows that butyrate increases global histone acetylation by preventing p300 recruitment to acetylated histones, rather than targeting specific genomic regions.

The paper introduces TS2CG version 2, a tool for building coarse-grained membrane structures with specific shapes and lateral organization, demonstrating its capabilities through various simulations.

This study investigates the phase separation of PKA RI regulatory subunits using NMR and MD simulations, revealing similar inter- and intra-molecular interactions driving this process.

The paper presents a workflow to create a comprehensive model of a mitochondrial crista junction using a coarse-grained representation and molecular modelling.

This paper introduces an enhanced G[o]Martini model that improves protein dynamics simulation and addresses inaccuracies in the Martini protein model through diverse case studies.

This paper introduces Martini 3 protein modeling, comparing three structure bias methods for maintaining protein structures in simulations.

This paper demonstrates hybrid polymer-lipid membranes that enable stable nanopore sensing in human serum, showing native-like nanopore behavior and efficient analyte sampling.

This study identifies a charged glutamate on VDAC1 and VDAC2 that interacts with HKI's N-terminal helix, revealing structural and mechanistic insights into their complex formation.

This study benchmarks coarse-grained simulation methods for analyzing enzyme transport tunnels, finding they efficiently capture tunnel geometry but vary in replicating all-atom dynamics.

The paper uses single-molecule optical tweezers to study the dynamics and interdomain interactions of the ABC transporter OpuA in lipid nanodiscs.

Shocker is a molecular dynamics tool that accelerates osmotic shock simulations by relocating water particles, enabling efficient study of membrane deformations in various systems.

This study uses molecular dynamics simulations to show that membrane curvature affects lipid sorting and phase behavior in complex ways beyond traditional models.

This paper introduces a DNA-based tool called SMS to generate controlled liposome shapes like stomatocytes and dumbbells, compatible with protein reconstitution.

The paper shows a mutation in CcpA improves fitness in Lactococcus lactis by reprogramming transporters, revealing membrane occupancy as a constraint.