Bottom-up coarse-graining: Principles and perspectives

J Jin, AJ Pak, AEP Durumeric, TD Loose… - Journal of chemical …, 2022 - ACS Publications
Large-scale computational molecular models provide scientists a means to investigate the
effect of microscopic details on emergent mesoscopic behavior. Elucidating the relationship …

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 …

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 …

Protein–ligand binding with the coarse-grained Martini model

PCT Souza, S Thallmair, P Conflitti… - Nature …, 2020 - nature.com
The detailed understanding of the binding of small molecules to proteins is the key for the
development of novel drugs or to increase the acceptance of substrates by enzymes …

Rescaling protein-protein interactions improves Martini 3 for flexible proteins in solution

FE Thomasen, T Skaalum, A Kumar… - Nature …, 2024 - nature.com
Multidomain proteins with flexible linkers and disordered regions play important roles in
many cellular processes, but characterizing their conformational ensembles is difficult. We …

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 …

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 …

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 …

The martini model in materials science

R Alessandri, F Grünewald, SJ Marrink - Advanced Materials, 2021 - Wiley Online Library
The Martini model, a coarse‐grained force field initially developed with biomolecular
simulations in mind, has found an increasing number of applications in the field of soft …

Microscopic Understanding of the Granular Structure and the Swelling of PEDOT: PSS

M Modarresi, A Mehandzhiyski, M Fahlman… - …, 2020 - ACS Publications
The conjugated polymer poly (3, 4-ethylenedioxythiophene) polymerized and stabilized in
the presence of polystyrenesulfonate (best known as PEDOT: PSS) is a working horse of …