Machine learning for chemical reactions
M Meuwly - Chemical Reviews, 2021 - ACS Publications
Machine learning (ML) techniques applied to chemical reactions have a long history. The
present contribution discusses applications ranging from small molecule reaction dynamics …
present contribution discusses applications ranging from small molecule reaction dynamics …
Loop dynamics and the evolution of enzyme activity
In the early 2000s, Tawfik presented his 'New View'on enzyme evolution, highlighting the
role of conformational plasticity in expanding the functional diversity of limited repertoires of …
role of conformational plasticity in expanding the functional diversity of limited repertoires of …
Advances in ultrahigh-throughput screening for directed enzyme evolution
U Markel, KD Essani, V Besirlioglu, J Schiffels… - Chemical Society …, 2020 - pubs.rsc.org
Enzymes are versatile catalysts and their synthetic potential has been recognized for a long
time. In order to exploit their full potential, enzymes often need to be re-engineered or …
time. In order to exploit their full potential, enzymes often need to be re-engineered or …
Biomolecular QM/MM simulations: What are some of the “burning issues”?
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. Considering the tremendous degree of success, including recognition by a …
Evolution of dynamical networks enhances catalysis in a designer enzyme
Activation heat capacity is emerging as a crucial factor in enzyme thermoadaptation, as
shown by the non-Arrhenius behaviour of many natural enzymes. However, its physical …
shown by the non-Arrhenius behaviour of many natural enzymes. However, its physical …
Designing better enzymes: Insights from directed evolution
Highlights•Enzymes can be created by computational design and directed
evolution.•Insights from directed evolution:•Active-site organization by H-bonding networks …
evolution.•Insights from directed evolution:•Active-site organization by H-bonding networks …
Temperature, dynamics, and enzyme-catalyzed reaction rates
VL Arcus, AJ Mulholland - Annual review of biophysics, 2020 - annualreviews.org
We review the adaptations of enzyme activity to different temperatures. Psychrophilic (cold-
adapted) enzymes show significantly different activation parameters (lower activation …
adapted) enzymes show significantly different activation parameters (lower activation …
Computational enzyme redesign: large jumps in function
Rising demands for enzymes in biotechnological applications have fueled efforts to tailor
their properties towards desired functions, such as activity, selectivity, and stability …
their properties towards desired functions, such as activity, selectivity, and stability …
Enzyme evolution and the temperature dependence of enzyme catalysis
Experiments and biomolecular simulations are revealing new and unexpected details of
how enzymes are adapted to specific temperatures. These findings are elucidating enzyme …
how enzymes are adapted to specific temperatures. These findings are elucidating enzyme …
From random to rational: improving enzyme design through electric fields, second coordination sphere interactions, and conformational dynamics
SS Chaturvedi, D Bím, CZ Christov… - Chemical Science, 2023 - pubs.rsc.org
Enzymes are versatile and efficient biological catalysts that drive numerous cellular
processes, motivating the development of enzyme design approaches to tailor catalysts for …
processes, motivating the development of enzyme design approaches to tailor catalysts for …