Alchemical Free Energy Calculations on Membrane-Associated Proteins
Membrane proteins have diverse functions within cells and are well-established drug
targets. The advances in membrane protein structural biology have revealed drug and lipid …
targets. The advances in membrane protein structural biology have revealed drug and lipid …
Overlay databank unlocks data-driven analyses of biomolecules for all
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 …
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
Cholesterol is a central building block in biomembranes, where it induces orientational
order, slows diffusion, renders the membrane stiffer, and drives domain formation. Molecular …
order, slows diffusion, renders the membrane stiffer, and drives domain formation. Molecular …
Effective inclusion of electronic polarization improves the description of electrostatic interactions: The prosECCo75 biomolecular force field
prosECCo75 is an optimized force field effectively incorporating electronic polarization via
charge scaling. It aims to enhance the accuracy of nominally nonpolarizable molecular …
charge scaling. It aims to enhance the accuracy of nominally nonpolarizable molecular …
Structure of POPC lipid bilayers in OPLS3e force field
It is crucial for molecular dynamics simulations of biomembranes that the force field
parameters give a realistic model of the membrane behavior. In this study, we examined the …
parameters give a realistic model of the membrane behavior. In this study, we examined the …
Emerging era of biomolecular membrane simulations: automated physically-justified force field development and quality-evaluated databanks
Molecular simulations of biological membranes and proxies thereof are entering a new era
characterized by several key aspects. Progress starts with the realization that the outcome of …
characterized by several key aspects. Progress starts with the realization that the outcome of …
Advancing Molecular Dynamics: Toward Standardization, Integration, and Data Accessibility in Structural Biology
Molecular dynamics (MD) simulations have become a valuable tool in structural biology,
offering insights into complex biological systems that are difficult to obtain through …
offering insights into complex biological systems that are difficult to obtain through …
Rotational decoupling between the hydrophilic and hydrophobic regions in lipid membranes
Cells use homeostatic mechanisms to ensure an optimal composition of distinct types of
lipids in cellular membranes. The hydrophilic region of biological lipid membranes is mainly …
lipids in cellular membranes. The hydrophilic region of biological lipid membranes is mainly …
Evaluating polarizable biomembrane simulations against experiments
Owing to the increase of available computational capabilities and the potential for providing
a more accurate description, polarizable molecular dynamics force fields are gaining …
a more accurate description, polarizable molecular dynamics force fields are gaining …
Elucidating the complex membrane binding of a protein with multiple anchoring domains using extHMMM
JJ Madsen, YZ Ohkubo - PLOS Computational Biology, 2024 - journals.plos.org
Membrane binding is a crucial mechanism for many proteins, but understanding the specific
interactions between proteins and membranes remains a challenging endeavor …
interactions between proteins and membranes remains a challenging endeavor …