Overlay databank unlocks data-driven analyses of biomolecules for all

AM Kiirikki, HS Antila, LS Bort, P Buslaev… - Nature …, 2024 - nature.com
Tools based on artificial intelligence (AI) are currently revolutionising many fields, yet their
applications are often limited by the lack of suitable training data in programmatically …

Quantitative comparison against experiments reveals imperfections in force fields' descriptions of popc–cholesterol interactions

M Javanainen, P Heftberger, JJ Madsen… - Journal of Chemical …, 2023 - ACS Publications
Cholesterol is a central building block in biomembranes, where it induces orientational
order, slows diffusion, renders the membrane stiffer, and drives domain formation. Molecular …

Pathways to a shiny future: Building the foundation for computational physical chemistry and biophysics in 2050

D Biriukov, R Vácha - ACS Physical Chemistry Au, 2024 - ACS Publications
In the last quarter-century, the field of molecular dynamics (MD) has undergone a
remarkable transformation, propelled by substantial enhancements in software, hardware …

Lipid Landscapes: Vibrational Spectroscopy for Decoding Membrane Complexity

X Chen, ZA Al-Mualem, CR Baiz - Annual Review of Physical …, 2024 - annualreviews.org
Cell membranes are incredibly complex environments containing hundreds of components.
Despite substantial advances in the past decade, fundamental questions related to lipid-lipid …

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 …

Charged small molecule binding to membranes in MD simulations evaluated against NMR experiments

R Nencini, OHS Ollila - The Journal of Physical Chemistry B, 2022 - ACS Publications
Interactions of charged molecules with biomembranes regulate many of their biological
activities, but their binding affinities to lipid bilayers are difficult to measure experimentally …

NMRlipids Databank makes data-driven analysis of biomembrane properties accessible for all

A Kiirikki, H Antila, L Bort, P Buslaev, F Fernando… - 2023 - chemrxiv.org
Cellular membrane lipid composition is implicated in diseases and controls major biological
functions, but membranes are difficult to study experimentally due to their intrinsic disorder …

Probing the dynamic landscape of peptides in molecular assemblies by synergized NMR experiments and MD simulations

R Nencini, MLG Regnier, SM Backlund… - Communications …, 2024 - nature.com
Peptides or proteins containing small biomolecular aggregates, such as micelles, bicelles,
droplets and nanodiscs, are pivotal in many fields ranging from structural biology to …

[HTML][HTML] Insights into the behavior of unsaturated diacylglycerols in mixed lipid bilayers in relation to protein kinase C activation—A molecular dynamics simulation …

S Heinonen, S Lautala, A Koivuniemi… - Biochimica et Biophysica …, 2022 - Elsevier
The lipid second messenger diacylglycerol (DAG) is known for its involvement in many types
of cellular signaling, especially as an endogenous agonist for protein kinase C (PKC) …