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 …

Big data need big theory too

PV Coveney, ER Dougherty… - … Transactions of the …, 2016 - royalsocietypublishing.org
The current interest in big data, machine learning and data analytics has generated the
widespread impression that such methods are capable of solving most problems without the …

Principles governing control of aggregation and dispersion of graphene and graphene oxide in polymer melts

JL Suter, RC Sinclair, PV Coveney - Advanced Materials, 2020 - Wiley Online Library
Controlling the structure of graphene and graphene oxide (GO) phases is vitally important
for any of its widespread intended applications: highly ordered arrangements of …

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 …

Relevance of molecular docking studies in drug designing

R Jakhar, M Dangi, A Khichi… - Current …, 2020 - ingentaconnect.com
Molecular Docking is used to positioning the computer-generated 3D structure of small
ligands into a receptor structure in a variety of orientations, conformations and positions …

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 …

Fast, accurate, and reliable protocols for routine calculations of protein–ligand binding affinities in drug design projects using AMBER GPU-TI with ff14SB/GAFF

X He, S Liu, TS Lee, B Ji, VH Man, DM York… - ACS omega, 2020 - ACS Publications
Accurate prediction of the absolute or relative protein–ligand binding affinity is one of the
major tasks in computer-aided drug design projects, especially in the stage of lead …

Uncertainty quantification in classical molecular dynamics

S Wan, RC Sinclair… - … Transactions of the …, 2021 - royalsocietypublishing.org
Molecular dynamics simulation is now a widespread approach for understanding complex
systems on the atomistic scale. It finds applications from physics and chemistry to …

In silico modeling and scoring of PROTAC-mediated ternary complex poses

J Liao, X Nie, IC Unarta, SS Ericksen… - Journal of Medicinal …, 2022 - ACS Publications
Proteolysis targeting chimeras (PROTACs) are molecules that induce protein degradation
via formation of ternary complexes between an E3 ubiquitin ligase and a target protein. The …

Graphene–graphene interactions: friction, superlubricity, and exfoliation

RC Sinclair, JL Suter, PV Coveney - Advanced Materials, 2018 - Wiley Online Library
Graphite's lubricating properties due to the “weak” interactions between individual layers
have long been known. However, these interactions are not weak enough to allow graphite …