ArticleReaction chemistry & engineering2019
Revealing quantum mechanical effects in enzyme catalysis with large-scale electronic structure simulation.
Article in Reaction chemistry & engineering, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
20 citing papers in PubMed, 43 citations in OpenAlex.
- QuantumPDB: A Workflow for High-Throughput Quantum Cluster Model Generation from Protein Structures.Journal of chemical information and modeling · 2026Article
- Article
- All Roads Lead to Carbinolamine: QM/MM Study of Enzymatic C-N Bond Cleavage in Anaerobic Glycyl Radical Enzyme Choline Trimethylamine-Lyase (CutC).The journal of physical chemistry. B · 2025Article
- Quick-and-Easy Validation of Protein-Ligand Binding Models Using Fragment-Based Semiempirical Quantum Chemistry.Journal of chemical information and modeling · 2025Article
- Utilizing Molecular Dynamics Simulations, Machine Learning, Cryo-EM, and NMR Spectroscopy to Predict and Validate Protein Dynamics.International journal of molecular sciences · 2024Review
- Mutexa: A Computational Ecosystem for Intelligent Protein Engineering.Journal of chemical theory and computation · 2023Review
- Targeting the human gut microbiome with small-molecule inhibitors.Nature reviews. Chemistry · 2023Review
- Alleviating the unwanted effects of oxidative stress on Aβ clearance: a review of related concepts and strategies for the development of computational modelling.Translational neurodegeneration · 2023Review
- Data-driven enzyme engineering to identify function-enhancing enzymes.Protein engineering, design & selection : PEDS · 2023Review
- Role of Enzyme and Active Site Conformational Dynamics in the Catalysis by α-Amylase Explored with QM/MM Molecular Dynamics.Journal of chemical information and modeling · 2022Article
- Factors That Determine the Variation of Equilibrium and Kinetic Properties of QM/MM Enzyme Simulations: QM Region, Conformation, and Boundary Condition.Journal of chemical theory and computation · 2022Article
- Current and Emerging Tools of Computational Biology To Improve the Detoxification of Mycotoxins.Applied and environmental microbiology · 2022Article
- The MOBH35 Metal-Organic Barrier Heights Reconsidered: Performance of Local-Orbital Coupled Cluster Approaches in Different Static Correlation Regimes.Journal of chemical theory and computation · 2022Article
- Molecular basis of C-S bond cleavage in the glycyl radical enzyme isethionate sulfite-lyase.Cell chemical biology · 2021Article
- Cheminformatic quantum mechanical enzyme model design: A catechol-O-methyltransferase case study.Biophysical journal · 2021Article
- Computational analysis of deleterious single nucleotide polymorphisms in catechol O-Methyltransferase conferring risk to post-traumatic stress disorder.Journal of psychiatric research · 2021Article
- When are two hydrogen bonds better than one? Accurate first-principles models explain the balance of hydrogen bond donors and acceptors found in proteins.Chemical science · 2021Article
- Hydrogen deuterium exchange defines catalytically linked regions of protein flexibility in the catecholProceedings of the National Academy of Sciences of the United States of America · 2020Article
- Article
- Linear Response Functions of Densities and Spin Densities for Systematic Modeling of the QM/MM Approach for Mono- and Poly-Nuclear Transition Metal Systems.Molecules (Basel, Switzerland) · 2019Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Enzymes have evolved to facilitate challenging reactions at ambient conditions with specificity seldom matched by other catalysts. Computational modeling provides valuable insight into catalytic mechanism, and the large size of enzymes mandates multi-scale, quantum mechanical-molecular mechanical (QM/MM) simulations. Although QM/MM plays an essential role in balancing simulation cost to enable sampling with full QM treatment needed to understand electronic structure in enzyme active sites, the relative importance of these two strategies for understanding enzyme mechanism is not well known. We explore challenges in QM/MM for studying the reactivity and stability of three diverse enzymes: i) Mg
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.