QM/MM methods for biomolecular systems

HM Senn, W Thiel - Angewandte Chemie International Edition, 2009 - Wiley Online Library
Two are better than one: Quantum mechanics/molecular mechanics (QM/MM) methods are
the state‐of‐the‐art computational technique for treating reactive and other “electronic” …

Modeling the kinetics of bimolecular reactions

A Fernández-Ramos, JA Miller, SJ Klippenstein… - Chemical …, 2006 - ACS Publications
This review is concerned with the theoretical and computational modeling of bimolecular
reactions, especially with generally applicable methods for kinetics (ie, overall rates as …

QM/MM methods for biological systems

HM Senn, W Thiel - Atomistic approaches in modern biology: from …, 2007 - Springer
Thirty years after the seminal contribution by Warshel and Levitt, we review the state of the
art of combined quantum-mechanics/molecular-mechanics (QM/MM) methods, with a focus …

Multidimensional tunneling, recrossing, and the transmission coefficient for enzymatic reactions

J Pu, J Gao, DG Truhlar - Chemical reviews, 2006 - ACS Publications
Although many aspects of enzyme catalysis have been constructively analyzed, 1-52 there
are still many aspects that are imperfectly understood. Of particular interest in this regard are …

Multiscale QM/MM Simulations Identify the Roles of Asp239 and 1-OH···Nucleophile in Transition State Stabilization in Arabidopsis thaliana Cell-Wall Invertase 1

W Meelua, T Wanjai, N Thinkumrob… - Journal of Chemical …, 2023 - ACS Publications
Arabidopsis thaliana cell-wall invertase 1 (AtCWIN1), a key enzyme in sucrose metabolism
in plants, catalyzes the hydrolysis of sucrose into fructose and glucose. AtCWIN1 belongs to …

Dynamic and electrostatic effects on the reaction catalyzed by HIV-1 protease

A Krzeminska, V Moliner… - Journal of the American …, 2016 - ACS Publications
HIV-1 Protease (HIV-1 PR) is one of the three enzymes essential for the replication process
of HIV-1 virus, which explains why it has been the main target for design of drugs against …

Large-scale QM/MM free energy simulations of enzyme catalysis reveal the influence of charge transfer

HJ Kulik - Physical Chemistry Chemical Physics, 2018 - pubs.rsc.org
Hybrid quantum mechanical–molecular mechanical (QM/MM) simulations provide key
insights into enzyme structure–function relationships. Numerous studies have demonstrated …

Insights on the Origin of Catalysis on Glycine N-Methyltransferase from Computational Modeling

K Swiderek, I Tuñón, IH Williams… - Journal of the American …, 2018 - ACS Publications
The origin of enzyme catalysis remains a question of debate despite much intense study. We
report a QM/MM theoretical study of the SN2 methyl transfer reaction catalyzed by a glycine …

QM/MM‐Methoden für biomolekulare Systeme

HM Senn, W Thiel - Angewandte Chemie, 2009 - Wiley Online Library
Quantenmechanische/molekülmechanische (QM/MM‐) Verfahren sind die Methode der
Wahl für die theoretische Behandlung reaktiver oder anderer elektronischer Prozesse in …

Protein conformational landscapes and catalysis. Influence of active site conformations in the reaction catalyzed by L-lactate dehydrogenase

K Swiderek, I Tunon, S Marti, V Moliner - ACS catalysis, 2015 - ACS Publications
In the past decade, L-Lactate Dehydrogenase (LDH) has become an extremely useful
marker in both clinical diagnosis and in monitoring the course of many human diseases. It …