Two decades of Martini: Better beads, broader scope

SJ Marrink, L Monticelli, MN Melo… - Wiley …, 2023‏ - Wiley Online Library
The Martini model, a coarse‐grained force field for molecular dynamics simulations, has
been around for nearly two decades. Originally developed for lipid‐based systems by the …

Coacervate droplets for synthetic cells

Z Lin, T Beneyton, JC Baret, N Martin - Small Methods, 2023‏ - Wiley Online Library
The design and construction of synthetic cells–human‐made microcompartments that mimic
features of living cells–have experienced a real boom in the past decade. While many efforts …

Pragmatic coarse-graining of proteins: models and applications

L Borges-Araújo, I Patmanidis, AP Singh… - Journal of Chemical …, 2023‏ - ACS Publications
The molecular details involved in the folding, dynamics, organization, and interaction of
proteins with other molecules are often difficult to assess by experimental techniques …

Improving Martini 3 for disordered and multidomain proteins

FE Thomasen, F Pesce, MA Roesgaard… - Journal of chemical …, 2022‏ - ACS Publications
Coarse-grained molecular dynamics simulations are a useful tool to determine
conformational ensembles of proteins. Here, we show that the coarse-grained force field …

Chemically specific coarse‐graining of polymers: methods and prospects

S Dhamankar, MA Webb - Journal of Polymer Science, 2021‏ - Wiley Online Library
Coarse‐grained (CG) modeling is an invaluable tool for the study of polymers and other soft
matter systems due to the span of spatiotemporal scales that typify their physics and …

Martini 3 coarse-grained force field for carbohydrates

F Grünewald, MH Punt, EE Jefferys… - Journal of Chemical …, 2022‏ - ACS Publications
The Martini 3 force field is a full reparametrization of the Martini coarse-grained model for
biomolecular simulations. Due to the improved interaction balance, it allows for a more …

Toward understanding lipid reorganization in RNA lipid nanoparticles in acidic environments

A Garaizar, D Díaz-Oviedo, N Zablowsky… - Proceedings of the …, 2024‏ - pnas.org
The use of lipid nanoparticles (LNPs) for therapeutic RNA delivery has gained significant
interest, particularly highlighted by recent milestones such as the approval of Onpattro and …

Advances in the study of supercooled water

P Gallo, J Bachler, LE Bove, R Böhmer… - The European Physical …, 2021‏ - Springer
In this review, we report recent progress in the field of supercooled water. Due to its
uniqueness, water presents numerous anomalies with respect to most simple liquids …

Facilitating CG simulations with MAD: The MArtini database server

C Hilpert, L Beranger, PCT Souza… - Journal of chemical …, 2023‏ - ACS Publications
The MArtini Database (MAD-https://mad. ibcp. fr) is a web server designed for the sharing of
structures and topologies of molecules parametrized with the Martini coarse-grained (CG) …

Assessing the Martini 3 protein model: A review of its path and potential

L Borges-Araújo, GP Pereira, M Valério… - Biochimica et Biophysica …, 2024‏ - Elsevier
Coarse-grained (CG) protein models have become indispensable tools for studying many
biological protein details, from conformational dynamics to the organization of protein macro …