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” …

The role of quantum chemistry in covalent inhibitor design

LM Mihalovits, GG Ferenczy… - International Journal of …, 2022 - Wiley Online Library
The recent ascent of targeted covalent inhibitors (TCI) in drug discovery brings new
opportunities and challenges to quantum chemical reactivity calculations supporting …

Biomolecular QM/MM simulations: What are some of the “burning issues”?

Q Cui, T Pal, L Xie - The Journal of Physical Chemistry B, 2021 - ACS Publications
QM/MM simulations have become an indispensable tool in many chemical and biochemical
investigations. Considering the tremendous degree of success, including recognition by a …

Investigations of enzyme-catalysed reactions with combined quantum mechanics/molecular mechanics (QM/MM) methods

KE Ranaghan, AJ Mulholland - International Reviews in Physical …, 2010 - Taylor & Francis
Combined quantum mechanics/molecular mechanics (QM/MM or QM-MM) methods are an
excellent approach for modelling the mechanisms of enzyme-catalysed reactions. QM/MM …

Electrostatic Preorganization in Three Distinct Heterogeneous Proteasome β-Subunits

S Ferrer, V Moliner, K Świderek - ACS catalysis, 2024 - ACS Publications
The origin of the enzyme's powerful role in accelerating chemical reactions is one of the
most critical and still widely discussed questions. It is already accepted that enzymes impose …

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 …

Impact of the Warhead of Dipeptidyl Keto Michael Acceptors on the Inhibition Mechanism of Cysteine Protease Cathepsin L

A Fernández-de-la-Pradilla, S Royo… - ACS …, 2023 - ACS Publications
Cathepsin L (CatL) is a lysosomal cysteine protease whose activity has been related to
several human pathologies. However, although preclinical trials using CatL inhibitors were …

Reaction Path-Force Matching in Collective Variables: Determining Ab Initio QM/MM Free Energy Profiles by Fitting Mean Force

B Kim, R Snyder, M Nagaraju, Y Zhou… - Journal of chemical …, 2021 - ACS Publications
First-principles determination of free energy profiles for condensed-phase chemical
reactions is hampered by the daunting costs associated with configurational sampling on ab …

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 …