Cations in motion: QM/MM studies of the dynamic and electrostatic roles of H+ and Mg2+ ions in enzyme reactions

D Berta, PJ Buigues, M Badaoui, E Rosta - Current Opinion in Structural …, 2020 - Elsevier
Highlights•Computational tools are essential in discovering mechanistic details of enzyme
reactions at sub-atomic resolution, providing information on proton and ion movements and …

Impact of Warhead Modulations on the Covalent Inhibition of SARS-CoV-2 Mpro Explored by QM/MM Simulations

S Martí, K Arafet, A Lodola, AJ Mulholland… - ACS …, 2021 - ACS Publications
The COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus-2,
SARS-CoV-2, shows the need for effective antiviral treatments. Here, we present a …

QM/MM study reveals novel mechanism of KRAS and KRASG12R catalyzed GTP hydrolysis

X Yan, L Zhu, Q Li, Y Tian, J Qiu, X Liu… - International Journal of …, 2025 - Elsevier
As a crucial drug target, KRAS can regulate most cellular processes involving guanosine
triphosphate (GTP) hydrolysis. However, the mechanism of GTP hydrolysis has remained …

Examination of the performance of semiempirical methods in QM/MM studies of the SN2-like reaction of an adenylyl group transfer catalysed by ANT4′

S Martí, V Moliner, K Świderek - Theoretical Chemistry Accounts, 2019 - Springer
Quantum mechanical (QM) semiempirical methods (SMs), combined with molecular
mechanics (MM) force fields, are extensively used in theoretical studies of enzymatic …