Regulation of membrane protein structure and function by their lipid nano-environment
I Levental, E Lyman - Nature Reviews Molecular Cell Biology, 2023 - nature.com
Transmembrane proteins comprise~ 30% of the mammalian proteome, mediating
metabolism, signalling, transport and many other functions required for cellular life. The …
metabolism, signalling, transport and many other functions required for cellular life. The …
Molecular dynamics simulations in drug discovery and pharmaceutical development
Molecular dynamics (MD) simulations have become increasingly useful in the modern drug
development process. In this review, we give a broad overview of the current application …
development process. In this review, we give a broad overview of the current application …
[HTML][HTML] Scalable molecular dynamics on CPU and GPU architectures with NAMD
NAMD is a molecular dynamics program designed for high-performance simulations of very
large biological objects on CPU-and GPU-based architectures. NAMD offers scalable …
large biological objects on CPU-and GPU-based architectures. NAMD offers scalable …
Computational modeling of realistic cell membranes
Cell membranes contain a large variety of lipid types and are crowded with proteins,
endowing them with the plasticity needed to fulfill their key roles in cell functioning. The …
endowing them with the plasticity needed to fulfill their key roles in cell functioning. The …
PyLipID: a python package for analysis of protein–lipid interactions from molecular dynamics simulations
Lipids play important modulatory and structural roles for membrane proteins. Molecular
dynamics simulations are frequently used to provide insights into the nature of these protein …
dynamics simulations are frequently used to provide insights into the nature of these protein …
Characterization of lipid–protein interactions and lipid-mediated modulation of membrane protein function through molecular simulation
The cellular membrane constitutes one of the most fundamental compartments of a living
cell, where key processes such as selective transport of material and exchange of …
cell, where key processes such as selective transport of material and exchange of …
Structural and thermodynamic framework for PIEZO1 modulation by small molecules
Mechanosensitive PIEZO channels constitute potential pharmacological targets for multiple
clinical conditions, spurring the search for potent chemical PIEZO modulators. Among them …
clinical conditions, spurring the search for potent chemical PIEZO modulators. Among them …
Open-channel structure of a pentameric ligand-gated ion channel reveals a mechanism of leaflet-specific phospholipid modulation
JT Petroff, NM Dietzen, E Santiago-McRae… - Nature …, 2022 - nature.com
Pentameric ligand-gated ion channels (pLGICs) mediate synaptic transmission and are
sensitive to their lipid environment. The mechanism of phospholipid modulation of any …
sensitive to their lipid environment. The mechanism of phospholipid modulation of any …
Standard Binding Free-Energy Calculations: How Far Are We from Automation?
Recent success stories suggest that in silico protein–ligand binding free-energy calculations
are approaching chemical accuracy. However, their widespread application remains limited …
are approaching chemical accuracy. However, their widespread application remains limited …
Comparison of receptor–ligand restraint schemes for alchemical absolute binding free energy calculations
Alchemical absolute binding free energy calculations are of increasing interest in drug
discovery. These calculations require restraints between the receptor and ligand to restrict …
discovery. These calculations require restraints between the receptor and ligand to restrict …