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 …

Coarse-grained protein models and their applications

S Kmiecik, D Gront, M Kolinski, L Wieteska… - Chemical …, 2016 - ACS Publications
The traditional computational modeling of protein structure, dynamics, and interactions
remains difficult for many protein systems. It is mostly due to the size of protein …

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 …

Structural basis of NINJ1-mediated plasma membrane rupture in cell death

M Degen, JC Santos, K Pluhackova, G Cebrero… - Nature, 2023 - nature.com
Eukaryotic cells can undergo different forms of programmed cell death, many of which
culminate in plasma membrane rupture as the defining terminal event,,,,,–. Plasma …

Bioactive scaffolds with enhanced supramolecular motion promote recovery from spinal cord injury

Z Álvarez, AN Kolberg-Edelbrock, IR Sasselli… - Science, 2021 - science.org
The signaling of cells by scaffolds of synthetic molecules that mimic proteins is known to be
effective in the regeneration of tissues. Here, we describe peptide amphiphile …

More bang for your buck: Improved use of GPU nodes for GROMACS 2018

C Kutzner, S Páll, M Fechner… - Journal of …, 2019 - Wiley Online Library
We identify hardware that is optimal to produce molecular dynamics (MD) trajectories on
Linux compute clusters with the GROMACS 2018 simulation package. Therefore, we …

Simulation of FUS protein condensates with an adapted coarse-grained model

Z Benayad, S von Bulow, LS Stelzl… - Journal of chemical …, 2020 - ACS Publications
Disordered proteins and nucleic acids can condense into droplets that resemble the
membraneless organelles observed in living cells. MD simulations offer a unique tool to …

Lipid–protein interactions are unique fingerprints for membrane proteins

V Corradi, E Mendez-Villuendas, HI Ingólfsson… - ACS central …, 2018 - ACS Publications
Cell membranes contain hundreds of different proteins and lipids in an asymmetric
arrangement. Our current understanding of the detailed organization of cell membranes …

Artificial extracellular matrix scaffolds of mobile molecules enhance maturation of human stem cell-derived neurons

Z Álvarez, JA Ortega, K Sato, IR Sasselli… - Cell stem cell, 2023 - cell.com
Human induced pluripotent stem cell (hiPSC) technologies offer a unique resource for
modeling neurological diseases. However, iPSC models are fraught with technical …

Enhancing molecular n‐type doping of donor–acceptor copolymers by tailoring side chains

J Liu, L Qiu, R Alessandri, X Qiu, G Portale… - Advanced …, 2018 - Wiley Online Library
In this contribution, for the first time, the molecular n‐doping of a donor–acceptor (D–A)
copolymer achieving 200‐fold enhancement of electrical conductivity by rationally tailoring …