ArticleBiophysical journal2021
Cheminformatic quantum mechanical enzyme model design: A catechol-O-methyltransferase case study.
Article in Biophysical journal, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Article
- Computational Investigation of GNMT-Catalyzed Methyl Transfer Reaction: Integrating MD, QM, and ML Approaches.Journal of computational chemistry · 2026Article
- QuantumPDB: A Workflow for High-Throughput Quantum Cluster Model Generation from Protein Structures.Journal of chemical information and modeling · 2026Article
- Quantum medicine: A quantum-mechanical framework for redox biology, disease and precision medicine.Clinical and translational medicine · 2026Review
- Density-Functionalized QM/MM Delivers Chemical Accuracy For Solvated Systems.Journal of chemical theory and computation · 2025Article
- Mechanistic Insights into SAM-Dependent Methyltransferases: A Review of Computational Approaches.International journal of molecular sciences · 2025Review
- Convergent Protocols for Computing Protein-Ligand Interaction Energies Using Fragment-Based Quantum Chemistry.Journal of chemical theory and computation · 2025Article
- Quick-and-Easy Validation of Protein-Ligand Binding Models Using Fragment-Based Semiempirical Quantum Chemistry.Journal of chemical information and modeling · 2025Article
- The influence of model building schemes and molecular dynamics sampling on QM-cluster models: the chorismate mutase case study.Physical chemistry chemical physics : PCCP · 2024Article
- The GlycineThe journal of physical chemistry. B · 2023Article
- A Case Study of the Glycoside Hydrolase Enzyme Mechanism Using an Automated QM-Cluster Model Building Toolkit.Frontiers in chemistry · 2022Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To accurately simulate the inner workings of an enzyme active site with quantum mechanics (QM), not only must the reactive species be included in the model but also important surrounding residues, solvent, or coenzymes involved in crafting the microenvironment. Our lab has been developing the Residue Interaction Network Residue Selector (RINRUS) toolkit to utilize interatomic contact network information for automated, rational residue selection and QM-cluster model generation. Starting from an x-ray crystal structure of catechol-O-methyltransferase, RINRUS was used to construct a series of QM-cluster models. The reactant, product, and transition state of the methyl transfer reaction were computed for a total of 550 models, and the resulting free energies of activation and reaction were used to evaluate model convergence. RINRUS-designed models with only 200-300 atoms are shown to converge. RINRUS will serve as a cornerstone for improved and automated cheminformatics-based enzyme model design.
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