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 …

Multifaceted computational modeling in glycoscience

S Perez, O Makshakova - Chemical Reviews, 2022 - ACS Publications
Glycoscience assembles all the scientific disciplines involved in studying various molecules
and macromolecules containing carbohydrates and complex glycans. Such an ensemble …

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 …

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) …

Extending the Martini 3 coarse-grained force field to carbohydrates

V Lutsyk, P Wolski, W Plazinski - Journal of Chemical Theory and …, 2022 - ACS Publications
Carbohydrates play an essential role in a large number of chemical and biochemical
processes. High structural diversity and conformational heterogeneity make it problematic to …

Structure and dynamics of the SARS‐CoV‐2 envelope protein monomer

A Kuzmin, P Orekhov, R Astashkin… - Proteins: Structure …, 2022 - Wiley Online Library
Coronaviruses, especially severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2),
present an ongoing threat to human wellbeing. Consequently, elucidation of molecular …

Allosteric activation of T cell antigen receptor signaling by quaternary structure relaxation

AL Lanz, G Masi, N Porciello, A Cohnen, D Cipria… - Cell reports, 2021 - cell.com
The mechanism of T cell antigen receptor (TCR-CD3) signaling remains elusive. Here, we
identify mutations in the transmembrane region of TCRβ or CD3ζ that augment peptide …

Molecular dynamics simulations for rationalizing polymer bioconjugation strategies: Challenges, recent developments, and future opportunities

J Kehrein, C Sotriffer - ACS Biomaterials Science & Engineering, 2023 - ACS Publications
The covalent modification of proteins with polymers is a well-established method for
improving the pharmacokinetic properties of therapeutically valuable biologics. The …

Boundary Lubrication Performance of Polyelectrolyte–Surfactant Complexes on Biomimetic Surfaces

E Weiand, PH Koenig, F Rodriguez-Ropero, Y Roiter… - Langmuir, 2024 - ACS Publications
Aqueous mixtures of oppositely charged polyelectrolytes and surfactants are useful in many
industrial applications, such as shampoos and hair conditioners. In this work, we investigate …