Alchemical Enhanced Sampling with Optimized Phase Space Overlap
An alchemical enhanced sampling (ACES) method has recently been introduced to facilitate
importance sampling in free energy simulations. The method achieves enhanced sampling …
importance sampling in free energy simulations. The method achieves enhanced sampling …
Adsorption of Flavonoids in a Transcriptional Regulator TtgR: Relative Binding Free Energies and Intermolecular Interactions
Antimicrobial resistance in bacteria often arises from their ability to actively identify and
expel toxic compounds. The bacterium strain Pseudomonas putida DOT-T1E utilizes its …
expel toxic compounds. The bacterium strain Pseudomonas putida DOT-T1E utilizes its …
Molecular simulations to investigate the impact of N6-methylation in RNA recognition: Improving accuracy and precision of binding free energy prediction
V Piomponi, M Krepl, J Sponer… - The Journal of Physical …, 2024 - ACS Publications
N6-Methyladenosine (m6A) is a prevalent RNA post-transcriptional modification that plays
crucial roles in RNA stability, structural dynamics, and interactions with proteins. The YT521 …
crucial roles in RNA stability, structural dynamics, and interactions with proteins. The YT521 …
Binding Selectivity Analysis from Alchemical Receptor Hopping and Ligand Swapping Free Energy Calculations
S Azimi, E Gallicchio - arXiv preprint arXiv:2402.06887, 2024 - arxiv.org
We present receptor-hopping and ligand-swapping free energy estimation protocols based
on the Alchemical Transfer Method (ATM) to model the binding selectivity of a set of ligands …
on the Alchemical Transfer Method (ATM) to model the binding selectivity of a set of ligands …