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 …
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
Molecular dynamics (MD) has evolved into a ubiquitous, versatile and powerful
computational method for fundamental research in science branches such as biology …
computational method for fundamental research in science branches such as biology …
Universal QM/MM approaches for general nanoscale applications
Quantum mechanics/molecular mechanics (QM/MM) hybrid models allow one to address
chemical phenomena in complex molecular environments. Whereas this modeling approach …
chemical phenomena in complex molecular environments. Whereas this modeling approach …
Rapid, accurate, precise and reproducible ligand–protein binding free energy prediction
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 …
of a molecule to a target biomacromolecule. Until recently, the accurate prediction of binding …
Vibrational spectroscopy by means of first‐principles molecular dynamics simulations
Vibrational spectroscopy is one of the most important experimental techniques for the
characterization of molecules and materials. Spectroscopic signatures retrieved in …
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
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 …
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 …
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 …
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
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 …
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 …
the potential of these DNA materials, a fundamental understanding of their structure and …