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 …

Computational modeling of realistic cell membranes

SJ Marrink, V Corradi, PCT Souza, HI Ingolfsson… - Chemical …, 2019‏ - ACS Publications
Cell membranes contain a large variety of lipid types and are crowded with proteins,
endowing them with the plasticity needed to fulfill their key roles in cell functioning. The …

Martini 3: a general purpose force field for coarse-grained molecular dynamics

PCT Souza, R Alessandri, J Barnoud, S Thallmair… - Nature …, 2021‏ - nature.com
The coarse-grained Martini force field is widely used in biomolecular simulations. Here we
present the refined model, Martini 3 (http://cgmartini. nl), with an improved interaction …

Multiscale simulations of biological membranes: the challenge to understand biological phenomena in a living substance

G Enkavi, M Javanainen, W Kulig, T Róg… - Chemical …, 2019‏ - ACS Publications
Biological membranes are tricky to investigate. They are complex in terms of molecular
composition and structure, functional over a wide range of time scales, and characterized by …

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 …

Martini 3 coarse-grained force field for cholesterol

L Borges-Araújo, AC Borges-Araújo… - Journal of Chemical …, 2023‏ - ACS Publications
Cholesterol plays a crucial role in biomembranes by regulating various properties, such as
fluidity, rigidity, permeability, and organization of lipid bilayers. The latest version of the …

CHARMM-GUI Membrane Builder: Past, Current, and Future Developments and Applications

S Feng, S Park, YK Choi, W Im - Journal of chemical theory and …, 2023‏ - ACS Publications
Molecular dynamics simulations of membranes and membrane proteins serve as
computational microscopes, revealing coordinated events at the membrane interface. As G …

Structure of the human signal peptidase complex reveals the determinants for signal peptide cleavage

AM Liaci, B Steigenberger, PCT de Souza, S Tamara… - Molecular cell, 2021‏ - cell.com
The signal peptidase complex (SPC) is an essential membrane complex in the endoplasmic
reticulum (ER), where it removes signal peptides (SPs) from a large variety of secretory pre …

[HTML][HTML] Not only in silico drug discovery: Molecular modeling towards in silico drug delivery formulations

T Casalini - Journal of Controlled Release, 2021‏ - Elsevier
The use of methods at molecular scale for the discovery of new potential active ligands, as
well as previously unknown binding sites for target proteins, is now an established reality …

Flux: Overcoming scheduling challenges for exascale workflows

DH Ahn, N Bass, A Chu, J Garlick, M Grondona… - Future Generation …, 2020‏ - Elsevier
Many emerging scientific workflows that target high-end HPC systems require complex
interplay with the resource and job management software (RJMS). However, portable …