An updated review of computer‐aided drug design and its application to COVID‐19

AB Gurung, MA Ali, J Lee, MA Farah… - BioMed research …, 2021 - Wiley Online Library
The recent outbreak of the deadly coronavirus disease 19 (COVID‐19) pandemic poses
serious health concerns around the world. The lack of approved drugs or vaccines continues …

Molecular dynamics simulations of ionic liquids and electrolytes using polarizable force fields

D Bedrov, JP Piquemal, O Borodin… - Chemical …, 2019 - ACS Publications
Many applications in chemistry, biology, and energy storage/conversion research rely on
molecular simulations to provide fundamental insight into structural and transport properties …

[HTML][HTML] Modern quantum chemistry with [Open] Molcas

F Aquilante, J Autschbach, A Baiardi… - The Journal of …, 2020 - pubs.aip.org
MOLCAS/OpenMolcas is an ab initio electronic structure program providing a large set of
computational methods from Hartree–Fock and density functional theory to various …

Boltzmann generators: Sampling equilibrium states of many-body systems with deep learning

F Noé, S Olsson, J Köhler, H Wu - Science, 2019 - science.org
INTRODUCTION Statistical mechanics aims to compute the average behavior of physical
systems on the basis of their microscopic constituents. For example, what is the probability …

[HTML][HTML] A suite of tutorials for the WESTPA rare-events sampling software [Article v1. 0]

AT Bogetti, B Mostofian, A Dickson… - Living journal of …, 2019 - ncbi.nlm.nih.gov
The weighted ensemble (WE) strategy has been demonstrated to be highly efficient in
generating pathways and rate constants for rare events such as protein folding and protein …

CHARMM-GUI nanomaterial modeler for modeling and simulation of nanomaterial systems

YK Choi, NR Kern, S Kim, K Kanhaiya… - Journal of chemical …, 2021 - ACS Publications
Molecular modeling and simulation are invaluable tools for nanoscience that predict
mechanical, physicochemical, and thermodynamic properties of nanomaterials and provide …

Molecular simulation for food protein–ligand interactions: A comprehensive review on principles, current applications, and emerging trends

Z **, Z Wei - Comprehensive Reviews in Food Science and …, 2024 - Wiley Online Library
In recent years, investigations on molecular interaction mechanisms between food proteins
and ligands have attracted much interest. The interaction mechanisms can supply much …

CHARMM-GUI PDB manipulator: various PDB structural modifications for biomolecular modeling and simulation

SJ Park, N Kern, T Brown, J Lee, W Im - Journal of Molecular Biology, 2023 - Elsevier
Molecular modeling and simulation play important roles in biomedical research as they
provide molecular-level insight into the underlying mechanisms of biological functions that …

Polarizable embedding QM/MM: the future gold standard for complex (bio) systems?

M Bondanza, M Nottoli, L Cupellini… - Physical Chemistry …, 2020 - pubs.rsc.org
Nowadays, hybrid QM/MM approaches are widely used to study (supra) molecular systems
embedded in complex biological matrices. However, in their common formulation, mutual …

Time-resolved terahertz–Raman spectroscopy reveals that cations and anions distinctly modify intermolecular interactions of water

V Balos, NK Kaliannan, H Elgabarty, M Wolf… - Nature Chemistry, 2022 - nature.com
The solvation of ions changes the physical, chemical and thermodynamic properties of
water, and the microscopic origin of this behaviour is believed to be ion-induced …