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Collective variable-based enhanced sampling: From human learning to machine learning
H Fu, H Bian, X Shao, W Cai - The journal of physical chemistry …, 2024 - ACS Publications
Enhanced-sampling algorithms relying on collective variables (CVs) are extensively
employed to study complex (bio) chemical processes that are not amenable to brute-force …
employed to study complex (bio) chemical processes that are not amenable to brute-force …
[HTML][HTML] In vitro and in silico studies of antimicrobial saponins: A review
J Li, V Monje-Galvan - Processes, 2023 - mdpi.com
Antibiotics are important drugs for the treatment of microbial infections and related diseases.
However, due to the abuse of antibiotics, drug resistance has become a serious and urgent …
However, due to the abuse of antibiotics, drug resistance has become a serious and urgent …
One Descriptor to Fold Them All: Harnessing Intuition and Machine Learning to Identify Transferable Lasso Peptide Reaction Coordinates
Identifying optimal reaction coordinates for complex conformational changes and protein
folding remains an outstanding challenge. This study combines collective variable (CV) …
folding remains an outstanding challenge. This study combines collective variable (CV) …
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 …
Molecular dynamics simulations for rationalizing polymer bioconjugation strategies: challenges, recent developments, and future opportunities
J Kehrein, C Sotriffer - ACS Biomaterials Science & Engineering, 2023 - ACS Publications
The covalent modification of proteins with polymers is a well-established method for
improving the pharmacokinetic properties of therapeutically valuable biologics. The …
improving the pharmacokinetic properties of therapeutically valuable biologics. The …
Unlocking bacterial defense: exploring the potent inhibition of NorA efflux pump by coumarin derivatives in Staphylococcus aureus
The occurrence of bacterial resistance has been increasing, compromising the treatment of
various infections. The high virulence of Staphylococcus aureus allows for the maintenance …
various infections. The high virulence of Staphylococcus aureus allows for the maintenance …
[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 …
[HTML][HTML] Mycolactone A vs. B: Multiscale Simulations Reveal the Roles of Localization and Association in Isomer-Specific Toxicity
Mycolactone is an exotoxin produced by Mycobacterium ulcerans that causes the neglected
tropical skin disease Buruli ulcer. This toxin inhibits the Sec61 translocon in the endoplasmic …
tropical skin disease Buruli ulcer. This toxin inhibits the Sec61 translocon in the endoplasmic …
Leveraging machine learning-guided molecular simulations coupled with experimental data to decipher membrane binding mechanisms of aminosterols
Understanding the molecular mechanisms of the interactions between specific compounds
and cellular membranes is essential for numerous biotechnological applications, including …
and cellular membranes is essential for numerous biotechnological applications, including …
Can membrane composition traffic toxins? Mycolactone and preferential membrane interactions
Mycolactone is a cytotoxic and immunosuppressive macrolide produced by Mycobacterium
ulcerans and the sole causative agent of the neglected tropical skin disease Buruli ulcer …
ulcerans and the sole causative agent of the neglected tropical skin disease Buruli ulcer …