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 …

Applied machine learning as a driver for polymeric biomaterials design

SM McDonald, EK Augustine, Q Lanners… - Nature …, 2023 - nature.com
Polymers are ubiquitous to almost every aspect of modern society and their use in medical
products is similarly pervasive. Despite this, the diversity in commercial polymers used in …

Molecular dynamics simulation of an entire cell

JA Stevens, F Grünewald, PAM van Tilburg… - Frontiers in …, 2023 - frontiersin.org
The ultimate microscope, directed at a cell, would reveal the dynamics of all the cell's
components with atomic resolution. In contrast to their real-world counterparts …

Martini 3 coarse‐grained force field: small molecules

R Alessandri, J Barnoud, AS Gertsen… - Advanced Theory …, 2022 - Wiley Online Library
The recent re‐parametrization of the Martini coarse‐grained force field, Martini 3, improved
the accuracy of the model in predicting molecular packing and interactions in molecular …

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 …

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 …

[HTML][HTML] Engineering poly-and micelleplexes for nucleic acid delivery–A reflection on their endosomal escape

B Winkeljann, DC Keul, OM Merkel - Journal of Controlled Release, 2023 - Elsevier
For the longest time, the field of nucleic acid delivery has remained skeptical whether or not
polycationic drug carrier systems would ever make it into clinical practice. Yet, with the …

A user's guide to machine learning for polymeric biomaterials

TA Meyer, C Ramirez, MJ Tamasi, AJ Gormley - ACS Polymers Au, 2022 - ACS Publications
The development of novel biomaterials is a challenging process, complicated by a design
space with high dimensionality. Requirements for performance in the complex biological …

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) …

[HTML][HTML] Molecular architecture and dynamics of SARS-CoV-2 envelope by integrative modeling

W Pezeshkian, F Grünewald, O Narykov, S Lu… - Structure, 2023 - cell.com
Despite tremendous efforts, the exact structure of SARS-CoV-2 and related
betacoronaviruses remains elusive. SARS-CoV-2 envelope is a key structural component of …