MDverse, shedding light on the dark matter of molecular dynamics simulations

JKS Tiemann, M Szczuka, L Bouarroudj, M Oussaren… - Elife, 2024 - elifesciences.org
The rise of open science and the absence of a global dedicated data repository for
molecular dynamics (MD) simulations has led to the accumulation of MD files in generalist …

Effective Inclusion of Electronic Polarization Improves the Description of Electrostatic Interactions: The prosECCo75 Biomolecular Force Field

R Nencini, C Tempra, D Biriukov… - Journal of Chemical …, 2024 - ACS Publications
prosECCo75 is an optimized force field effectively incorporating electronic polarization via
charge scaling. It aims to enhance the accuracy of nominally nonpolarizable molecular …

Evaluating polarizable biomembrane simulations against experiments

HS Antila, S Dixit, B Kav, JJ Madsen… - Journal of Chemical …, 2024 - ACS Publications
Owing to the increase of available computational capabilities and the potential for providing
a more accurate description, polarizable molecular dynamics force fields are gaining …

Simulating Bacterial Membrane Models at the Atomistic Level: A Force Field Comparison

A Blanco-González, A Wurl… - Journal of Chemical …, 2024 - ACS Publications
Molecular dynamics (MD) simulations are currently an indispensable tool to understand both
the dynamic and nanoscale organization of cell membrane models. A large number of …

Probing the dynamic landscape of peptides in membrane mimics by synergized NMR experiments and MD simulations

S Ollila, R Nencini, M Regnier, S Backlund, E Mantzari… - 2023 - researchsquare.com
Dynamic interactions between peptides and lipid membranes are crucial in many biological
processes and biomedical applications. Monitoring peptide dynamics in a membrane …

[HTML][HTML] Dynamic Nature of Staphylococcus aureus Type I Signal Peptidases

JJ Madsen, W Yu - bioRxiv, 2024 - ncbi.nlm.nih.gov
Molecular dynamics simulations are used to interrogate the dynamic nature of
Staphylococcus aureus Type I signal peptidases, SpsA and SpsB, including the impact of …

[HTML][HTML] Efficient calculation of orientation-dependent lipid dynamics from membrane simulations

M Doktorova, G Khelashvili, MF Brown - bioRxiv, 2024 - ncbi.nlm.nih.gov
Molecular dynamics simulations of lipid membranes have become increasingly impactful in
biophysics because they offer atomistic resolution of structural fluctuations in relation to their …

Sampling Bottleneck in Validating Membrane Dynamics

M Doktorova, G Khelashvili, MF Brown - bioRxiv, 2023 - biorxiv.org
Molecular dynamics (MD) simulations have become increasingly impactful in membrane
biophysics because they offer atomistic resolution into the atomistic fluctuations of lipid …

Effective Inclusion of Electronic Polarization Improves the Description of Electrostatic Interactions: The prosECCo75 Biomolecular Force Field

C Tempra, R Nencini, D Biriukov - 2024 - dlib.hust.edu.vn
prosECCo75 is an optimized force field effectively incorporating electronic polarization via
charge scaling. It aims to enhance the accuracy of nominally nonpolarizable molecular …

Probing the dynamic landscape of peptides in membrane mimics by synergized NMR experiments and MD simulations

R Nencini, M Regnier, S Backlund, E Mantzari, C Dunn… - 2023 - chemrxiv.org
Dynamic interactions between peptides and lipid membranes are crucial in many biological
processes and biomedical applications However, monitoring of peptide dynamics in a …