ArticleThe journal of physical chemistry. B2021
Exploring the Minimum-Energy Pathways and Free-Energy Profiles of Enzymatic Reactions with QM/MM Calculations.
Article in The journal of physical chemistry. B, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Smoother Alchemical Transformations via Enveloping Distribution Sampling for Free-Energy Estimation.Journal of chemical theory and computation · 2026Article
- Proton Transfer through a Charged Conduit in Respiratory Complex I: Long-Range Effects and Conformational Gating.Journal of chemical information and modeling · 2025Article
- High-performance QM/MM Enhanced Sampling Molecular Dynamics Simulations with GENESIS SPDYN and QSimulate-QM.Journal of chemical theory and computation · 2025Article
- Efficient Training of Neural Network Potentials for Chemical and Enzymatic Reactions by Continual Learning.Journal of chemical theory and computation · 2025Article
- Multiscale calculations reveal new insights into the reaction mechanism between KRASComputational and structural biotechnology journal · 2024Article
- Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment.Chemical reviews · 2024Review
- Computational Insights into Amide Bond Formation Catalyzed by the Condensation Domain of Nonribosomal Peptide Synthetases.ACS omega · 2024Article
- GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models.The journal of physical chemistry. B · 2024Article
- Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development.ACS omega · 2024Review
- Unraveling the catalytic mechanism of SARS-CoV-2 papain-like protease with allosteric modulation of C270 mutation using multiscale computational approaches.Chemical science · 2023Article
- Hybrid Quantum Mechanical/Molecular Mechanical Methods For Studying Energy Transduction in Biomolecular Machines.Annual review of biophysics · 2023Review
- Use of multistate Bennett acceptance ratio method for free-energy calculations from enhanced sampling and free-energy perturbation.Biophysical reviews · 2022Review
- Mechanistic Insights into Enzyme Catalysis from Explaining Machine-Learned Quantum Mechanical and Molecular Mechanical Minimum Energy Pathways.ACS physical chemistry Au · 2022Article
- Computational Analysis on the Allostery of Tryptophan Synthase: Relationship between α/β-Ligand Binding and Distal Domain Closure.The journal of physical chemistry. B · 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
- Modeling Catalysis in Allosteric Enzymes: Capturing Conformational Consequences.Topics in catalysis · 2022Article
- Retinal Vibrations in Bacteriorhodopsin are Mechanically Harmonic but Electrically Anharmonic: Evidence From Overtone and Combination Bands.Frontiers in molecular biosciences · 2021Article
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Understanding molecular mechanisms of enzymatic reactions is of vital importance in biochemistry and biophysics. Here, we introduce new functions of hybrid quantum mechanical/molecular mechanical (QM/MM) calculations in the GENESIS program to compute the minimum-energy pathways (MEPs) and free-energy profiles of enzymatic reactions. For this purpose, an interface in GENESIS is developed to utilize a highly parallel electronic structure program, QSimulate-QM (https://qsimulate.com), calling it as a shared library from GENESIS. Second, algorithms to search the MEP are implemented, combining the string method (E et al.
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