标题
QM/MM free energy simulations: recent progress and challenges
作者
关键词
-
出版物
MOLECULAR SIMULATION
Volume 42, Issue 13, Pages 1056-1078
出版商
Informa UK Limited
发表日期
2016-07-06
DOI
10.1080/08927022.2015.1132317
参考文献
相关参考文献
注意：仅列出部分参考文献，下载原文获取全部文献信息。- Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States
- (2015) Elizabeth Brunk et al. CHEMICAL REVIEWS
- Sampling reactive pathways with random walks in chemical space: Applications to molecular dissociation and catalysis
- (2015) Scott Habershon JOURNAL OF CHEMICAL PHYSICS
- DFTB3 Parametrization for Copper: The Importance of Orbital Angular Momentum Dependence of Hubbard Parameters
- (2015) Michael Gaus et al. Journal of Chemical Theory and Computation
- Conformational Preadjustment in Aqueous Claisen Rearrangement Revealed by SITS-QM/MM MD Simulations
- (2015) Jun Zhang et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Microscopic basis for kinetic gating in cytochrome c oxidase: insights from QM/MM analysis
- (2015) Puja Goyal et al. Chemical Science
- Biological Responses to Engineered Nanomaterials: Needs for the Next Decade
- (2015) Catherine J. Murphy et al. ACS Central Science
- Accuracy-rate tradeoffs: how do enzymes meet demands of selectivity and catalytic efficiency?
- (2014) Dan S Tawfik CURRENT OPINION IN CHEMICAL BIOLOGY
- Computer aided enzyme design and catalytic concepts
- (2014) Maria P Frushicheva et al. CURRENT OPINION IN CHEMICAL BIOLOGY
- The robustness and innovability of protein folds
- (2014) Ágnes Tóth-Petróczy et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- QM/MM Modelling of Drug-Metabolizing Enzymes
- (2014) Richard Lonsdale et al. CURRENT TOPICS IN MEDICINAL CHEMISTRY
- Quantum mechanical/molecular mechanical studies of zinc hydrolases
- (2014) Dingguo Xu et al. INTERNATIONAL REVIEWS IN PHYSICAL CHEMISTRY
- Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states
- (2014) Hao Wu et al. JOURNAL OF CHEMICAL PHYSICS
- Computing the Free Energy Barriers for Less by Sampling with a Coarse Reference Potential while Retaining Accuracy of the Target Fine Model
- (2014) Nikolay V. Plotnikov Journal of Chemical Theory and Computation
- Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes
- (2014) Gerhard König et al. Journal of Chemical Theory and Computation
- Reaction Path Force Matching: A New Strategy of Fitting Specific Reaction Parameters for Semiempirical Methods in Combined QM/MM Simulations
- (2014) Yan Zhou et al. Journal of Chemical Theory and Computation
- Comparison between Mean Forces and Swarms-of-Trajectories String Methods
- (2014) Luca Maragliano et al. Journal of Chemical Theory and Computation
- Acceleration of Ab Initio QM/MM Calculations under Periodic Boundary Conditions by Multiscale and Multiple Time Step Approaches
- (2014) Kwangho Nam Journal of Chemical Theory and Computation
- Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme
- (2014) Vojtěch Mlýnský et al. Journal of Chemical Theory and Computation
- An Overview of Electrostatic Free Energy Computations for Solutions and Proteins
- (2014) Yen-Lin Lin et al. Journal of Chemical Theory and Computation
- Parameterization of the DFTB3 Method for Br, Ca, Cl, F, I, K, and Na in Organic and Biological Systems
- (2014) Maximilian Kubillus et al. Journal of Chemical Theory and Computation
- Parameterization of DFTB3/3OB for Sulfur and Phosphorus for Chemical and Biological Applications
- (2014) Michael Gaus et al. Journal of Chemical Theory and Computation
- Free Energies from Dynamic Weighted Histogram Analysis Using Unbiased Markov State Model
- (2014) Edina Rosta et al. Journal of Chemical Theory and Computation
- Integrated Hamiltonian Sampling: A Simple and Versatile Method for Free Energy Simulations and Conformational Sampling
- (2014) Toshifumi Mori et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Hydrated Excess Protons Can Create Their Own Water Wires
- (2014) Yuxing Peng et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Enzymatic Minimum Free Energy Path Calculations Using Swarms of Trajectories
- (2014) Melchor Sanchez-Martinez et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Parametrization of DFTB3/3OB for Magnesium and Zinc for Chemical and Biological Applications
- (2014) Xiya Lu et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Molecular Simulation of Water and Hydration Effects in Different Environments: Challenges and Developments for DFTB Based Models
- (2014) Puja Goyal et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Density functional tight binding: values of semi-empirical methods in an ab initio era
- (2014) Qiang Cui et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Well-Tempered Metadynamics Converges Asymptotically
- (2014) James F. Dama et al. PHYSICAL REVIEW LETTERS
- Conversion of Channelrhodopsin into a Light-Gated Chloride Channel
- (2014) J. Wietek et al. SCIENCE
- Leveraging structure for enzyme function prediction: methods, opportunities, and challenges
- (2014) Matthew P. Jacobson et al. TRENDS IN BIOCHEMICAL SCIENCES
- Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Methods in Computational Enzymology
- (2013) Marc W. van der Kamp et al. BIOCHEMISTRY
- Quantum mechanics/molecular mechanics dual Hamiltonian free energy perturbation
- (2013) Iakov Polyak et al. JOURNAL OF CHEMICAL PHYSICS
- An Explicit Consideration of Desolvation is Critical to Binding Free Energy Calculations of Charged Molecules at Ionic Surfaces
- (2013) Toshifumi Mori et al. Journal of Chemical Theory and Computation
- Charging Free Energy Calculations Using the Generalized Solvent Boundary Potential (GSBP) and Periodic Boundary Condition: A Comparative Analysis Using Ion Solvation and Oxidation Free Energy in Proteins
- (2013) Xiya Lu et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Stabilization of Different Types of Transition States in a Single Enzyme Active Site: QM/MM Analysis of Enzymes in the Alkaline Phosphatase Superfamily
- (2013) Guanhua Hou et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Systematic exploration of the mechanism of chemical reactions: the global reaction route mapping (GRRM) strategy using the ADDF and AFIR methods
- (2013) Satoshi Maeda et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Modeling catalytic promiscuity in the alkaline phosphatase superfamily
- (2013) Fernanda Duarte et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Changing hydration level in an internal cavity modulates the proton affinity of a key glutamate in cytochrome c oxidase
- (2013) P. Goyal et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Potential functional roles of DNA demethylation intermediates
- (2013) Chun-Xiao Song et al. TRENDS IN BIOCHEMICAL SCIENCES
- Density functional tight binding: application to organic and biological molecules
- (2013) Michael Gaus et al. Wiley Interdisciplinary Reviews-Computational Molecular Science
- A Modified QM/MM Hamiltonian with the Self-Consistent-Charge Density-Functional-Tight-Binding Theory for Highly Charged QM Regions
- (2012) Guanhua Hou et al. Journal of Chemical Theory and Computation
- The Solvation Structure of Na+ and K+ in Liquid Water Determined from High Level ab Initio Molecular Dynamics Simulations
- (2012) Christopher N. Rowley et al. Journal of Chemical Theory and Computation
- Parametrization and Benchmark of DFTB3 for Organic Molecules
- (2012) Michael Gaus et al. Journal of Chemical Theory and Computation
- Implementation of the Solvent Macromolecule Boundary Potential and Application to Model and Realistic Enzyme Systems
- (2012) Jan Zienau et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Convergence of QM/MM free-energy perturbations based on molecular-mechanics or semiempirical simulations
- (2012) Jimmy Heimdal et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Transmembrane Helix Assembly by Window Exchange Umbrella Sampling
- (2012) Soohyung Park et al. PHYSICAL REVIEW LETTERS
- Biological Phosphoryl-Transfer Reactions: Understanding Mechanism and Catalysis
- (2011) Jonathan K. Lassila et al. Annual Review of Biochemistry
- Free energy of conformational transition paths in biomolecules: The string method and its application to myosin VI
- (2011) Victor Ovchinnikov 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
- QM/MM Reweighting Free Energy SCF for Geometry Optimization on Extensive Free Energy Surface of Enzymatic Reaction
- (2011) Takahiro Kosugi et al. Journal of Chemical Theory and Computation
- Paradynamics: An Effective and Reliable Model for Ab Initio QM/MM Free-Energy Calculations and Related Tasks
- (2011) Nikolay V. Plotnikov et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Replica Exchange with Solute Scaling: A More Efficient Version of Replica Exchange with Solute Tempering (REST2)
- (2011) Lingle Wang et al. JOURNAL OF PHYSICAL CHEMISTRY B
- QM/MM Analysis Suggests That Alkaline Phosphatase (AP) and Nucleotide Pyrophosphatase/Phosphodiesterase Slightly Tighten the Transition State for Phosphate Diester Hydrolysis Relative to Solution: Implication for Catalytic Promiscuity in the AP Superfamily
- (2011) Guanhua Hou et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Simulations of Allosteric Motions in the Zinc Sensor CzrA
- (2011) Dhruva K. Chakravorty et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Demystifying DNA Demethylation
- (2011) C. S. Nabel et al. SCIENCE
- Metadynamics
- (2011) Alessandro Barducci et al. Wiley Interdisciplinary Reviews-Computational Molecular Science
- Structural and Functional Insights into the Myosin Motor Mechanism
- (2010) H. Lee Sweeney et al. Annual Review of Biophysics
- Proton-Coupled Electron Transfer in Cytochrome Oxidase
- (2010) Ville R. I. Kaila et al. CHEMICAL REVIEWS
- Coupled motions in enzyme catalysis
- (2010) Vishal C Nashine et al. CURRENT OPINION IN CHEMICAL BIOLOGY
- Free energy calculations using dual-level Born–Oppenheimer molecular dynamics
- (2010) Marius Retegan et al. JOURNAL OF CHEMICAL PHYSICS
- Good Practices in Free-Energy Calculations
- (2010) Andrew Pohorille et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase
- (2010) Chengqi Yi et al. NATURE
- Efficient Catalytic Promiscuity for Chemically Distinct Reactions
- (2009) Ann C. Babtie et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- QM/MM Methods for Biomolecular Systems
- (2009) Hans Martin Senn et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- P450 Enzymes: Their Structure, Reactivity, and Selectivity—Modeled by QM/MM Calculations
- (2009) Sason Shaik et al. CHEMICAL REVIEWS
- A selective integrated tempering method
- (2009) Lijiang Yang et al. JOURNAL OF CHEMICAL PHYSICS
- Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model
- (2009) Devleena Shivakumar et al. Journal of Chemical Theory and Computation
- CHARMM: The biomolecular simulation program
- (2009) B. R. Brooks et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Computations of Standard Binding Free Energies with Molecular Dynamics Simulations
- (2009) Yuqing Deng et al. JOURNAL OF PHYSICAL CHEMISTRY B
- The far reaches of enzymology
- (2009) Jesse G Zalatan et al. Nature Chemical Biology
- Free Energies of Chemical Reactions in Solution and in Enzymes with Ab Initio Quantum Mechanics/Molecular Mechanics Methods
- (2008) Hao Hu et al. Annual Review of Physical Chemistry
- Transition-Path Theory and Path-Finding Algorithms for the Study of Rare Events
- (2008) Weinan E et al. Annual Review of Physical Chemistry
- Proton Transfer in Carbonic Anhydrase Is Controlled by Electrostatics Rather than the Orientation of the Acceptor†
- (2008) Demian Riccardi et al. BIOCHEMISTRY
- Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: Sequential sampling and optimization on the potential of mean force surface
- (2008) Hao Hu et al. JOURNAL OF CHEMICAL PHYSICS
- An efficient method for the calculation of quantum mechanics/molecular mechanics free energies
- (2008) Christopher J. Woods et al. JOURNAL OF CHEMICAL PHYSICS
- An integrate-over-temperature approach for enhanced sampling
- (2008) Yi Qin Gao JOURNAL OF CHEMICAL PHYSICS
- Description of Phosphate Hydrolysis Reactions with the Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) Theory. 1. Parameterization
- (2008) Yang Yang et al. Journal of Chemical Theory and Computation
- Extensive Conformational Transitions Are Required to Turn On ATP Hydrolysis in Myosin
- (2008) Yang Yang et al. JOURNAL OF MOLECULAR BIOLOGY
- Finding Transition Pathways Using the String Method with Swarms of Trajectories
- (2008) Albert C. Pan et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Progress inAb InitioQM/MM Free-Energy Simulations of Electrostatic Energies in Proteins: Accelerated QM/MM Studies of pKa, Redox Reactions and Solvation Free Energies†
- (2008) Shina C. L. Kamerlin et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
- (2008) Alessandro Barducci et al. PHYSICAL REVIEW LETTERS
- Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science
- (2008) Alessandro Laio et al. REPORTS ON PROGRESS IN PHYSICS
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreCreate your own webinar
Interested in hosting your own webinar? Check the schedule and propose your idea to the Peeref Content Team.
Create Now