Combined QM/MM, Machine Learning Path Integral Approach to Compute Free Energy Profiles and Kinetic Isotope Effects in RNA Cleavage Reactions
出版年份 2022 全文链接
标题
Combined QM/MM, Machine Learning Path Integral Approach to Compute Free Energy Profiles and Kinetic Isotope Effects in RNA Cleavage Reactions
作者
关键词
-
出版物
Journal of Chemical Theory and Computation
Volume 18, Issue 7, Pages 4304-4317
出版商
American Chemical Society (ACS)
发表日期
2022-06-17
DOI
10.1021/acs.jctc.2c00151
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- (2022) Claudia L. Gómez-Flores et al. Journal of Chemical Theory and Computation
- A simplified charge projection scheme for long-range electrostatics in ab initio QM/MM calculations
- (2021) Xiaoliang Pan et al. JOURNAL OF CHEMICAL PHYSICS
- Reactive uptake of N2O5 by atmospheric aerosol is dominated by interfacial processes
- (2021) Mirza Galib et al. SCIENCE
- Using metadynamics to build neural network potentials for reactive events: the case of urea decomposition in water
- (2021) Manyi Yang et al. CATALYSIS TODAY
- Extension of the Variational Free Energy Profile and Multistate Bennett Acceptance Ratio Methods for High-Dimensional Potential of Mean Force Profile Analysis
- (2021) Timothy J. Giese et al. JOURNAL OF PHYSICAL CHEMISTRY A
- Machine Learning for Chemical Reactions
- (2021) Markus Meuwly CHEMICAL REVIEWS
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- (2021) Xiaoliang Pan et al. Journal of Chemical Theory and Computation
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- (2021) Jinzhe Zeng et al. Journal of Chemical Theory and Computation
- Affordable Ab Initio Path Integral for Thermodynamic Properties via Molecular Dynamics Simulations Using Semiempirical Reference Potential
- (2021) Yuanfei Xue et al. JOURNAL OF PHYSICAL CHEMISTRY A
- DP-GEN: A concurrent learning platform for the generation of reliable deep learning based potential energy models
- (2020) Yuzhi Zhang et al. COMPUTER PHYSICS COMMUNICATIONS
- Role of Microsolvation and Quantum Effects in the Accurate Prediction of Kinetic Isotope Effects: The Case of Hydrogen Atom Abstraction in Ethanol by Atomic Hydrogen in Aqueous Solution
- (2020) Suraj Kannath et al. Journal of Chemical Theory and Computation
- Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme
- (2020) Abir Ganguly et al. Nature Chemistry
- Accelerated Computation of Free Energy Profile at Ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semiempirical Reference Potential. 3. Gaussian Smoothing on Density-of-States
- (2020) Wenxin Hu et al. Journal of Chemical Theory and Computation
- Exploring the Chemical Space of Linear Alkane Pyrolysis via Deep Potential GENerator
- (2020) Jinzhe Zeng et al. ENERGY & FUELS
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- (2020) Denghui Lu et al. COMPUTER PHYSICS COMMUNICATIONS
- An Ontology for Facilitating Discussion of Catalytic Strategies of RNA-Cleaving Enzymes
- (2019) Philip C. Bevilacqua et al. ACS Chemical Biology
- Cleaning Up Mechanistic Debris Generated by Twister Ribozymes Using Computational RNA Enzymology
- (2019) Colin S. Gaines et al. ACS Catalysis
- DeePMD-kit: A deep learning package for many-body potential energy representation and molecular dynamics
- (2018) Han Wang et al. COMPUTER PHYSICS COMMUNICATIONS
- A GPU-Accelerated Parameter Interpolation Thermodynamic Integration Free Energy Method
- (2018) Timothy J. Giese et al. Journal of Chemical Theory and Computation
- Enzymatic Transition States and Drug Design
- (2018) Vern L. Schramm CHEMICAL REVIEWS
- Accelerated Computation of Free Energy Profile at ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semi-Empirical Reference Potential. I. Weighted Thermodynamics Perturbation
- (2018) Pengfei Li et al. Journal of Chemical Theory and Computation
- Efficient Strategy for the Calculation of Solvation Free Energies in Water and Chloroform at the Quantum Mechanical/Molecular Mechanical Level
- (2017) Meiting Wang et al. Journal of Chemical Information and Modeling
- Ambient-Potential Composite Ewald Method for ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation
- (2016) Timothy J. Giese et al. Journal of Chemical Theory and Computation
- Integration of kinetic isotope effect analyses to elucidate ribonuclease mechanism
- (2015) Michael E. Harris et al. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
- Enzyme transition states from theory and experiment
- (2015) Mike E. Harris et al. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
- Effect of Zn 2+ binding and enzyme active site on the transition state for RNA 2′-O-transphosphorylation interpreted through kinetic isotope effects
- (2015) Haoyuan Chen et al. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
- Heavy atom labeled nucleotides for measurement of kinetic isotope effects
- (2015) Benjamin P. Weissman et al. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
- New QM/MM implementation of the DFTB3 method in the gromacs package
- (2015) Tomáš Kubař et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Kinetic Isotope Effects in Multipath VTST: Application to a Hydrogen Abstraction Reaction
- (2015) Luis Simón-Carballido et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Nucleic Acid Catalysis: Metals, Nucleobases, and Other Cofactors
- (2014) W. Luke Ward et al. CHEMICAL REVIEWS
- Mechanistic Insights into RNA Transphosphorylation from Kinetic Isotope Effects and Linear Free Energy Relationships of Model Reactions
- (2014) Haoyuan Chen et al. CHEMISTRY-A EUROPEAN JOURNAL
- XSEDE: Accelerating Scientific Discovery
- (2014) John Towns et al. COMPUTING IN SCIENCE & ENGINEERING
- Altered (transition) states: mechanisms of solution and enzyme catalyzed RNA 2′-O-transphosphorylation
- (2014) Daniel L Kellerman et al. CURRENT OPINION IN CHEMICAL BIOLOGY
- Linear free energy relationships in RNA transesterification: theoretical models to aid experimental interpretations
- (2014) Ming Huang et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
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- (2013) Michele Ceriotti et al. COMPUTER PHYSICS COMMUNICATIONS
- PLUMED 2: New feathers for an old bird
- (2013) Gareth A. Tribello et al. COMPUTER PHYSICS COMMUNICATIONS
- Efficient methods and practical guidelines for simulating isotope effects
- (2013) Michele Ceriotti et al. JOURNAL OF CHEMICAL PHYSICS
- Roadmaps through Free Energy Landscapes Calculated Using the Multidimensional vFEP Approach
- (2013) Tai-Sung Lee et al. Journal of Chemical Theory and Computation
- Experimental and computational analysis of the transition state for ribonuclease A-catalyzed RNA 2'-O-transphosphorylation
- (2013) H. Gu et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Multi-path variational transition state theory for chemical reaction rates of complex polyatomic species: ethanol + OH reactions
- (2012) Jingjing Zheng et al. FARADAY DISCUSSIONS
- A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations
- (2012) Tai-Sung Lee et al. Journal of Chemical Theory and Computation
- Efficient First-Principles Calculation of the Quantum Kinetic Energy and Momentum Distribution of Nuclei
- (2012) Michele Ceriotti et al. PHYSICAL REVIEW LETTERS
- Characterization of the Reaction Path and Transition States for RNA Transphosphorylation Models from Theory and Experiment
- (2011) Kin-Yiu Wong et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- Biological Phosphoryl-Transfer Reactions: Understanding Mechanism and Catalysis
- (2011) Jonathan K. Lassila et al. Annual Review of Biochemistry
- Accelerating the convergence of path integral dynamics with a generalized Langevin equation
- (2011) Michele Ceriotti et al. JOURNAL OF CHEMICAL PHYSICS
- DFTB3: Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method (SCC-DFTB)
- (2011) Michael Gaus et al. Journal of Chemical Theory and Computation
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- (2011) Tao Yu et al. Chemical Science
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- (2009) Massimiliano Bonomi et al. COMPUTER PHYSICS COMMUNICATIONS
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- (2008) Yang Yang et al. Journal of Chemical Theory and Computation
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