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 …

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 …

[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 …

Towards chemical accuracy for alchemical free energy calculations with hybrid physics-based machine learning/molecular mechanics potentials

DA Rufa, HE Bruce Macdonald, J Fass, M Wieder… - BioRxiv, 2020 - biorxiv.org
Alchemical free energy methods with molecular mechanics (MM) force fields are now widely
used in the prioritization of small molecules for synthesis in structure-enabled drug discovery …

[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 …

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 …

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 …

Pandemic drugs at pandemic speed: infrastructure for accelerating COVID-19 drug discovery with hybrid machine learning-and physics-based simulations on high …

AP Bhati, S Wan, D Alfè, AR Clyde, M Bode… - Interface …, 2021 - royalsocietypublishing.org
The race to meet the challenges of the global pandemic has served as a reminder that the
existing drug discovery process is expensive, inefficient and slow. There is a major …

Reproducibility of free energy calculations across different molecular simulation software packages

HH Loeffler, S Bosisio… - Journal of chemical …, 2018 - ACS Publications
Alchemical free energy calculations are an increasingly important modern simulation
technique to calculate free energy changes on binding or solvation. Contemporary …

Artificial intelligence in drug design: algorithms, applications, challenges and ethics

AA Arabi - Future Drug Discovery, 2021 - Future Science
The discovery paradigm of drugs is rapidly growing due to advances in machine learning
(ML) and artificial intelligence (AI). This review covers myriad faces of AI and ML in drug …