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 …

[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 …

One Descriptor to Fold Them All: Harnessing Intuition and Machine Learning to Identify Transferable Lasso Peptide Reaction Coordinates

GCA da Hora, M Oh, JDM Nguyen… - The Journal of …, 2024 - ACS Publications
Identifying optimal reaction coordinates for complex conformational changes and protein
folding remains an outstanding challenge. This study combines collective variable (CV) …

tICA-Metadynamics for identifying slow dynamics in membrane permeation

M Oh, GCA Da Hora, JMJ Swanson - Journal of chemical theory …, 2023 - ACS Publications
Molecular simulations are commonly used to understand the mechanism of membrane
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 …

Unlocking bacterial defense: exploring the potent inhibition of NorA efflux pump by coumarin derivatives in Staphylococcus aureus

ALAR Martin, RLS Pereira, JE Rocha, PAM Farias… - Microbial …, 2024 - Elsevier
The occurrence of bacterial resistance has been increasing, compromising the treatment of
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

AMM Gomes, PJ Costa, M Machuqueiro - BBA advances, 2023 - Elsevier
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 …

[HTML][HTML] Mycolactone A vs. B: Multiscale Simulations Reveal the Roles of Localization and Association in Isomer-Specific Toxicity

JDM Nguyen, GCA da Hora, JMJ Swanson - Toxins, 2023 - mdpi.com
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 …

Leveraging machine learning-guided molecular simulations coupled with experimental data to decipher membrane binding mechanisms of aminosterols

S Muscat, S Errico, A Danani, F Chiti… - Journal of chemical …, 2024 - ACS Publications
Understanding the molecular mechanisms of the interactions between specific compounds
and cellular membranes is essential for numerous biotechnological applications, including …

Can membrane composition traffic toxins? Mycolactone and preferential membrane interactions

GCA da Hora, JDM Nguyen, JMJ Swanson - Biophysical Journal, 2022 - cell.com
Mycolactone is a cytotoxic and immunosuppressive macrolide produced by Mycobacterium
ulcerans and the sole causative agent of the neglected tropical skin disease Buruli ulcer …