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Hydrogenase enzymes and their synthetic models: the role of metal hydrides
Hydrogenase enzymes efficiently process H2 and protons at organometallic FeFe, NiFe, or
Fe active sites. Synthetic modeling of the many H2ase states has provided insight into …
Fe active sites. Synthetic modeling of the many H2ase states has provided insight into …
Mixed quantum mechanical/molecular mechanical molecular dynamics simulations of biological systems in ground and electronically excited states
The quantum nature of electrons and nuclei is manifested in countless biological events
including the rearrangements of electrons in biochemical reactions, electron and proton …
including the rearrangements of electrons in biochemical reactions, electron and proton …
Self-consistent determination of long-range electrostatics in neural network potentials
Abstract Machine learning has the potential to revolutionize the field of molecular simulation
through the development of efficient and accurate models of interatomic interactions. Neural …
through the development of efficient and accurate models of interatomic interactions. Neural …
The molecular mechanism of the catalase reaction
Catalases are ubiquitous enzymes that prevent cell oxidative damage by degrading
hydrogen peroxide to water and oxygen (2H2O2→ 2 H2O+ O2) with high efficiency. The …
hydrogen peroxide to water and oxygen (2H2O2→ 2 H2O+ O2) with high efficiency. The …
Metal–ligand interactions in drug design
The fast-growing body of experimental data on metalloenzymes and organometallic
compounds is fostering the exploitation of metal–ligand interactions for the design of new …
compounds is fostering the exploitation of metal–ligand interactions for the design of new …
Interaction of antibacterial compounds with RND efflux pumps in Pseudomonas aeruginosa
J Dreier, P Ruggerone - Frontiers in microbiology, 2015 - frontiersin.org
Pseudomonas aeruginosa infections are becoming increasingly difficult to treat due to
intrinsic antibiotic resistance and the propensity of this pathogen to accumulate diverse …
intrinsic antibiotic resistance and the propensity of this pathogen to accumulate diverse …
Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms
Quantum mechanics/molecular mechanics (QM/MM) methods offer a very appealing option
for the computational study of enzymatic reaction mechanisms, by separating the problem …
for the computational study of enzymatic reaction mechanisms, by separating the problem …
Catalytic metal ions and enzymatic processing of DNA and RNA
Conspectus Two-metal-ion-dependent nucleases cleave the phosphodiester bonds of
nucleic acids via the two-metal-ion (2M) mechanism. Several high-resolution X-ray …
nucleic acids via the two-metal-ion (2M) mechanism. Several high-resolution X-ray …
Modelling enzymatic mechanisms with QM/MM approaches: current status and future challenges
RP Magalhães, HS Fernandes… - Israel Journal of …, 2020 - Wiley Online Library
Quantum mechanics/molecular mechanics (QM/MM) methods are presently a well‐
established alternative for the study of enzymatic reaction mechanisms. They enable the …
established alternative for the study of enzymatic reaction mechanisms. They enable the …
Multiscale modeling of proteins
V Tozzini - Accounts of chemical research, 2010 - ACS Publications
The activity within a living cell is based on a complex network of interactions among
biomolecules, exchanging information and energy through biochemical processes. These …
biomolecules, exchanging information and energy through biochemical processes. These …