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 …

Molecular dynamics simulations in drug discovery and pharmaceutical development

OMH Salo-Ahen, I Alanko, R Bhadane, AMJJ Bonvin… - Processes, 2020 - mdpi.com
Molecular dynamics (MD) simulations have become increasingly useful in the modern drug
development process. In this review, we give a broad overview of the current application …

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 …

Emerging diversity in lipid–protein interactions

V Corradi, BI Sejdiu, H Mesa-Galloso… - Chemical …, 2019 - ACS Publications
Membrane lipids interact with proteins in a variety of ways, ranging from providing a stable
membrane environment for proteins to being embedded in to detailed roles in complicated …

Structural insight and development of EGFR tyrosine kinase inhibitors

T Amelia, RE Kartasasmita, T Ohwada, DH Tjahjono - Molecules, 2022 - mdpi.com
Lung cancer has a high prevalence, with a growing number of new cases and mortality
every year. Furthermore, the survival rate of patients with non-small-cell lung carcinoma …

Subcellular location defines GPCR signal transduction

A Radoux-Mergault, L Oberhauser, S Aureli… - Science …, 2023 - science.org
Intracellular G protein-coupled receptors (GPCRs) can be activated by permeant ligands,
which contributes to agonist selectivity. Opioid receptors (ORs) provide a notable example …

Excessive aggregation of membrane proteins in the Martini model

M Javanainen, H Martinez-Seara, I Vattulainen - PloS one, 2017 - journals.plos.org
The coarse-grained Martini model is employed extensively to study membrane protein
oligomerization. While this approach is exceptionally promising given its computational …

CHARMM‐GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides

PC Hsu, BMH Bruininks, D Jefferies… - 2017 - Wiley Online Library
A complex cell envelope, composed of a mixture of lipid types including
lipopolysaccharides, protects bacteria from the external environment. Clearly, the proteins …

Combining the MARTINI and structure-based coarse-grained approaches for the molecular dynamics studies of conformational transitions in proteins

AB Poma, M Cieplak… - Journal of Chemical Theory …, 2017 - ACS Publications
The application of coarse-grained (CG) models in biology is essential to access large length
and time scales required for the description of many biological processes. The ELNEDIN …

Large-Scale Conformational Changes and Protein Function: Breaking the in silico Barrier

L Orellana - Frontiers in molecular biosciences, 2019 - frontiersin.org
Large-scale conformational changes are essential to link protein structures with their
function at the cell and organism scale, but have been elusive both experimentally and …