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Aging mechanism of soman inhibited acetylcholinesterase.
Acetylcholinesterase (AChE) is a crucial enzyme in the cholinergic nervous system that hydrolyzes neurotransmitter acetylcholine (ACh) and terminates synaptic signals. The catalytic serine of AChEExpand
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Free energy calculation on enzyme reactions with an efficient iterative procedure to determine minimum energy paths on a combined ab initio QM/MM potential energy surface
A new practical approach to studying enzyme reactions by combining ab initio QM/MM calculations with free energy perturbation is presented. An efficient iterative optimization procedure has beenExpand
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A challenge for density functionals: Self-interaction error increases for systems with a noninteger number of electrons
The difficulty of widely used density functionals in describing the dissociation behavior of some homonuclear and heteronuclear diatomic radicals is analyzed. It is shown that the self-interactionExpand
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Role of the catalytic triad and oxyanion hole in acetylcholinesterase catalysis: an ab initio QM/MM study.
The initial step of the acylation reaction catalyzed by acetylcholinesterase (AChE) has been studied by a combined ab initio quantum mechanical/molecular mechanical (QM/MM) approach. The reactionExpand
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How does the cAMP-dependent protein kinase catalyze the phosphorylation reaction: an ab initio QM/MM study.
We have carried out density functional theory QM/MM calculations on the catalytic subunit of cAMP-dependent protein kinase (PKA). The QM/MM calculations indicate that the phosphorylation reactionExpand
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Catalytic mechanism and product specificity of the histone lysine methyltransferase SET7/9: an ab initio QM/MM-FE study with multiple initial structures.
  • P. Hu, Y. Zhang
  • Chemistry, Medicine
  • Journal of the American Chemical Society
  • 1 February 2006
Histone lysine methylation is emerging as an important mechanism to regulate chromatin structure and gene activity. To provide theoretical understanding of its reaction mechanism and productExpand
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Zinc chelation with hydroxamate in histone deacetylases modulated by water access to the linker binding channel.
It is of significant biological interest and medical importance to develop class- and isoform-selective histone deacetylase (HDAC) modulators. The impact of the linker component on HDAC inhibitionExpand
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Improving scoring‐docking‐screening powers of protein–ligand scoring functions using random forest
TLDR
We introduce a new scoring function for protein–ligand docking based on random forest, which can achieve superior performance in docking and screening power tests compared to classical scoring functions. Expand
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Catalytic reaction mechanism of acetylcholinesterase determined by Born-Oppenheimer ab initio QM/MM molecular dynamics simulations.
Acetylcholinesterase (AChE) is a remarkably efficient serine hydrolase responsible for the termination of impulse signaling at cholinergic synapses. By employing Born-Oppenheimer molecular dynamicsExpand
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