ReviewACS omega2024
Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development.
Review in ACS omega, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 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
33 citing papers in PubMed, 44 citations in OpenAlex.
- Engineering of fructose-6-phosphate aldolase for one-carbon conversion to mannitol in a designed biotransformation system.Synthetic and systems biotechnology · 2026Article
- Methods for the establishment of enzymatic mechanisms - from QM to ML.Chemical science · 2026Review
- Evaluating Mechanical-Embedding ML/MM for Predicting Mutation Effects in Chorismate Mutase Catalysis.Journal of chemical theory and computation · 2026Article
- Accurate and Time-Efficient Condensed-Phase Free Energy Simulations with Reaction Specific Δ-Machine Learning Potentials in CHARMM.Journal of chemical theory and computation · 2026Article
- A historical journey of metabolite-protein interaction discovery: from data harmonization to AI-driven prediction.Briefings in bioinformatics · 2026Review
- Distance-Restraint-Guided Diffusion Models for Sampling Protein Conformational Changes and Ligand Dissociation Pathways.Journal of chemical theory and computation · 2026Article
- Accelerating Quantum Mechanical/Molecular Mechanical (QM/MM) Simulations with Stochastic Iso-Kinetic Nosé-Hoover Multiple Time Step Integrator in CHARMM.The journal of physical chemistry. B · 2026Article
- Systematically Improvable and Locality Accelerated Enzymatic Reactivity Modeling: Toward Chemical Accuracy at Affordable Cost.Journal of chemical theory and computation · 2026Article
- Reactive carbonyl species in health and chronic disease: from methylglyoxal to an integrative network of metabolic regulation.Cardiovascular diabetology · 2026Review
- Predictive Chemical Kinetic Modeling: Where We Succeed, Where We Struggle, and What Comes Next.ACS engineering Au · 2026Review
- DFT study of frontier orbitals and NLO properties of a phenanthroline and nitrophenol complex.Scientific reports · 2026Article
- Experimental and In Silico Approaches to Study Carboxylesterase Substrate Specificity.Journal of xenobiotics · 2026Review
- Computational design of metallohydrolases.Nature · 2026Article
- Computational Innovations in Cancer Research and How Computing is Transforming Drug Discovery and Development: A Review.Mini reviews in medicinal chemistry · 2026Review
- Quantum medicine: A quantum-mechanical framework for redox biology, disease and precision medicine.Clinical and translational medicine · 2026Review
- Article
- Rational Engineering of Patchoulene Synthase fromInternational journal of molecular sciences · 2025Article
- Approaches for regulating enzyme activities: Recent advances in experiment and computation.Current opinion in structural biology · 2025Review
- Fermi calculations enable quick downselection of target genes and process optimization in photosynthetic systems.Plant physiology · 2025Review
- A Foundational Shift in Models for Enzyme Function.Journal of the American Chemical Society · 2025Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 4 institutions in 3 countries.
Funding
Abstract
Understanding enzyme mechanisms is essential for unraveling the complex molecular machinery of life. In this review, we survey the field of computational enzymology, highlighting key principles governing enzyme mechanisms and discussing ongoing challenges and promising advances. Over the years, computer simulations have become indispensable in the study of enzyme mechanisms, with the integration of experimental and computational exploration now established as a holistic approach to gain deep insights into enzymatic catalysis. Numerous studies have demonstrated the power of computer simulations in characterizing reaction pathways, transition states, substrate selectivity, product distribution, and dynamic conformational changes for various enzymes. Nevertheless, significant challenges remain in investigating the mechanisms of complex multistep reactions, large-scale conformational changes, and allosteric regulation. Beyond mechanistic studies, computational enzyme modeling has emerged as an essential tool for computer-aided enzyme design and the rational discovery of covalent drugs for targeted therapies. Overall, enzyme design/engineering and covalent drug development can greatly benefit from our understanding of the detailed mechanisms of enzymes, such as protein dynamics, entropy contributions, and allostery, as revealed by computational studies. Such a convergence of different research approaches is expected to continue, creating synergies in enzyme research. This review, by outlining the ever-expanding field of enzyme research, aims to provide guidance for future research directions and facilitate new developments in this important and evolving field.
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.