Dynamical reweighting for biased rare event simulations
Dynamical reweighting techniques aim to recover the correct molecular dynamics from a
simulation at a modified potential energy surface. They are important for unbiasing …
simulation at a modified potential energy surface. They are important for unbiasing …
Free energy methods for the description of molecular processes
C Chipot - Annual Review of Biophysics, 2023 - annualreviews.org
Efforts to combine theory and experiment to advance our knowledge of molecular processes
relevant to biophysics have been considerably enhanced by the contribution of statistical …
relevant to biophysics have been considerably enhanced by the contribution of statistical …
Membrane thickness, lipid phase and sterol type are determining factors in the permeability of membranes to small solutes
Cell membranes provide a selective semi-permeable barrier to the passive transport of
molecules. This property differs greatly between organisms. While the cytoplasmic …
molecules. This property differs greatly between organisms. While the cytoplasmic …
Drude polarizable lipid force field with explicit treatment of long-range dispersion: Parametrization and validation for saturated and monounsaturated zwitterionic lipids
Accurate empirical force fields of lipid molecules are a critical component of molecular
dynamics simulation studies aimed at investigating properties of monolayers, bilayers …
dynamics simulation studies aimed at investigating properties of monolayers, bilayers …
tICA-Metadynamics for Identifying Slow Dynamics in Membrane Permeation
Molecular simulations are commonly used to understand the mechanism of membrane
permeation of small molecules, particularly for biomedical and pharmaceutical applications …
permeation of small molecules, particularly for biomedical and pharmaceutical applications …
[HTML][HTML] Classical molecular dynamics
This issue of JCP highlights both developments in and applications of classical molecular
simulation in 67 articles. A recent issue of JCP focused on electronic structure software …
simulation in 67 articles. A recent issue of JCP focused on electronic structure software …
Predictions from First-Principles of Membrane Permeability to Small Molecules: How Useful Are They in Practice?
C Chipot - Journal of Chemical Information and Modeling, 2023 - ACS Publications
Predicting from first-principles the rate of passive permeation of small molecules across the
biological membrane represents a promising strategy for screening lead compounds …
biological membrane represents a promising strategy for screening lead compounds …
Recent experimental developments in studying passive membrane transport of drug molecules
M Sharifian Gh - Molecular Pharmaceutics, 2021 - ACS Publications
The ability to measure the passive membrane permeation of drug-like molecules is of
fundamental biological and pharmaceutical importance. Of significance, passive diffusion …
fundamental biological and pharmaceutical importance. Of significance, passive diffusion …
Combining SILCS and Artificial Intelligence for High-Throughput Prediction of the Passive Permeability of Drug Molecules
Membrane permeability of drug molecules plays a significant role in the development of new
therapeutic agents. Accordingly, methods to predict the passive permeability of drug …
therapeutic agents. Accordingly, methods to predict the passive permeability of drug …
[HTML][HTML] Recent advances on molecular dynamics-based techniques to address drug membrane permeability with atomistic detail
Several factors affect the passive membrane permeation of small molecules, including size,
charge, pH, or the presence of specific chemical groups. Understanding these features is …
charge, pH, or the presence of specific chemical groups. Understanding these features is …