ArticleChemistry Central journal2007
Chemical accuracy in QM/MM calculations on enzyme-catalysed reactions.
Article in Chemistry Central journal, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed.
- Simulating enzyme catalysis with electrostatically embedded machine learning potentials.Chemical science · 2026Article
- Mechanistic and Kinetic Insights into the Acylation Reaction of Hepatitis C Virus NS3/NS4A Serine Protease with NS4B/5A Substrate.Biomolecules · 2025Article
- Challenges and Advances in the Simulation of Targeted Covalent Inhibitors Using Quantum Computing.The journal of physical chemistry letters · 2025Review
- The Effects of Conformational Sampling and QM Region Size in QM/MM Simulations: An Adaptive QM/MM Study With Model Systems.Journal of computational chemistry · 2025Article
- Unraveling the Pivotal Roles of Various Metal Ion Centers in the Catalysis of Quercetin 2,4-Dioxygenases.Molecules (Basel, Switzerland) · 2023Article
- Exploring Routes to Enhance the Calculation of Free Energy Differences via Non-Equilibrium Work SQM/MM Switching Simulations Using Hybrid Charge Intermediates between MM and SQM Levels of Theory or Non-Linear Switching Schemes.Molecules (Basel, Switzerland) · 2023Article
- Efficiently Computing Excitations of Complex Systems: Linear-Scaling Time-Dependent Embedded Mean-Field Theory in Implicit Solvent.Journal of chemical theory and computation · 2022Article
- High throughput and quantitative enzymology in the genomic era.Current opinion in structural biology · 2021Review
- Towards reproducible computational drug discovery.Journal of cheminformatics · 2020Review
- Computational enzymology for degradation of chemical warfare agents: promising technologies for remediation processes.AIMS microbiology · 2017Article
- A comparison of X-ray and calculated structures of the enzyme MTH1.Journal of molecular modeling · 2016Article
- Application of a SCC-DFTB QM/MM approach to the investigation of the catalytic mechanism of fatty acid amide hydrolase.Journal of molecular modeling · 2011Article
- Biomolecular simulation and modelling: status, progress and prospects.Journal of the Royal Society, Interface · 2008Review
- Introduction. Biomolecular simulation.Journal of the Royal Society, Interface · 2008Article
- Analysis of polarization in QM/MM modelling of biologically relevant hydrogen bonds.Journal of the Royal Society, Interface · 2008Article
- Multiscale methods for macromolecular simulations.Current opinion in structural biology · 2008Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Combined quantum mechanics/molecular mechanics (QM/MM) modelling has the potential to answer fundamental questions about enzyme mechanisms and catalysis. Calculations using QM/MM methods can now predict barriers for enzyme-catalysed reactions with unprecedented, near chemical accuracy, i.e. to within 1 kcal/mol in the best cases. Quantitative predictions from first-principles calculations were only previously possible for very small molecules. At this level, quantitative, reliable predictions can be made about the mechanisms of enzyme-catalysed reactions. This development signals a new era of computational biochemistry.
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.