- Home
- Publications
- Publication Search
- Publication Details
Title
QM/MM free energy simulations: recent progress and challenges
Authors
Keywords
-
Journal
MOLECULAR SIMULATION
Volume 42, Issue 13, Pages 1056-1078
Publisher
Informa UK Limited
Online
2016-07-06
DOI
10.1080/08927022.2015.1132317
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- 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 the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
SearchAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started