Recognition in the domain of molecular chirality: from noncovalent interactions to separation of enantiomers

P Peluso, B Chankvetadze - Chemical Reviews, 2022 - ACS Publications
It is not a coincidence that both chirality and noncovalent interactions are ubiquitous in
nature and synthetic molecular systems. Noncovalent interactivity between chiral molecules …

[HTML][HTML] Classical and reactive molecular dynamics: Principles and applications in combustion and energy systems

Q Mao, M Feng, XZ Jiang, Y Ren, KH Luo… - Progress in Energy and …, 2023 - Elsevier
Molecular dynamics (MD) has evolved into a ubiquitous, versatile and powerful
computational method for fundamental research in science branches such as biology …

Universal QM/MM approaches for general nanoscale applications

KS Csizi, M Reiher - Wiley Interdisciplinary Reviews …, 2023 - Wiley Online Library
Quantum mechanics/molecular mechanics (QM/MM) hybrid models allow one to address
chemical phenomena in complex molecular environments. Whereas this modeling approach …

Rapid, accurate, precise and reproducible ligand–protein binding free energy prediction

S Wan, AP Bhati, SJ Zasada… - Interface …, 2020 - royalsocietypublishing.org
A central quantity of interest in molecular biology and medicine is the free energy of binding
of a molecule to a target biomacromolecule. Until recently, the accurate prediction of binding …

Vibrational spectroscopy by means of first‐principles molecular dynamics simulations

E Ditler, S Luber - Wiley Interdisciplinary Reviews …, 2022 - Wiley Online Library
Vibrational spectroscopy is one of the most important experimental techniques for the
characterization of molecules and materials. Spectroscopic signatures retrieved in …

[HTML][HTML] Design, synthesis, computational study and cytotoxic evaluation of some new quinazoline derivatives containing pyrimidine moiety

S Zare, L Emami, Z Faghih, F Zargari, Z Faghih… - Scientific reports, 2023 - nature.com
Quinazoline derivatives, as an important category of heterocyclic compounds, have received
much attention for the design and development of new drugs due to their various …

[HTML][HTML] Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks [article v1. 0]

DF Hahn, CI Bayly, ML Boby… - Living journal of …, 2022 - ncbi.nlm.nih.gov
Free energy calculations are rapidly becoming indispensable in structure-enabled drug
discovery programs. As new methods, force fields, and implementations are developed …

Large scale study of ligand–protein relative binding free energy calculations: actionable predictions from statistically robust protocols

AP Bhati, PV Coveney - Journal of Chemical Theory and …, 2022 - ACS Publications
The accurate and reliable prediction of protein–ligand binding affinities can play a central
role in the drug discovery process as well as in personalized medicine. Of considerable …

Ensembles are required to handle aleatoric and parametric uncertainty in molecular dynamics simulation

M Vassaux, S Wan, W Edeling… - Journal of chemical …, 2021 - ACS Publications
Classical molecular dynamics is a computer simulation technique that is in widespread use
across many areas of science, from physics and chemistry to materials, biology, and …

[HTML][HTML] Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations

K Ahmad, A Javed, C Lanphere, PV Coveney… - Nature …, 2023 - nature.com
DNA can be folded into rationally designed, unique, and functional materials. To fully realise
the potential of these DNA materials, a fundamental understanding of their structure and …