Optimizing the Calculation of Free Energy Differences in Nonequilibrium Work SQM/MM Switching Simulations

Biomolecular QM/MM Simulations: What Are Some of the “Burning Issues”?

(2021) Qiang Cui et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Harder, better, faster, stronger: Large-scale QM and QM/MM for predictive modeling in enzymes and proteins

(2021) Vyshnavi Vennelakanti et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Cations in motion: QM/MM studies of the dynamic and electrostatic roles of H+ and Mg2+ ions in enzyme reactions

(2020) Dénes Berta et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Multi-level free energy simulation with a staged transformation approach

(2020) Shingo Ito et al.   JOURNAL OF CHEMICAL PHYSICS

Atomic-level characterization of protein–protein association

(2019) Albert C. Pan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Good, the Bad, and the Ugly: “HiPen”, a New Dataset for Validating (S)QM/MM Free Energy Simulations

(2019) Fiona Kearns et al.   MOLECULES

Exploring binding mechanisms of VEGFR2 with three drugs lenvatinib, sorafenib, and sunitinib by molecular dynamics simulation and free energy calculation

(2019) Yu Wang et al.   Chemical Biology & Drug Design

Molecular mechanisms of the protein-protein interaction–regulated binding specificity of basic-region leucine zipper transcription factors

(2019) Qing Li et al.   JOURNAL OF MOLECULAR MODELING

Development of a Robust Indirect Approach for MM → QM Free Energy Calculations That Combines Force-Matched Reference Potential and Bennett’s Acceptance Ratio Methods

(2019) Timothy J. Giese et al.   Journal of Chemical Theory and Computation

On the convergence of multi-scale free energy simulations

(2018) Gerhard König et al.   MOLECULAR SIMULATION

Large-scale QM/MM free energy simulations of enzyme catalysis reveal the influence of charge transfer

(2018) Heather J. Kulik   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

The catalytic mechanism of the Serine Hydroxymethyltransferase – a computational ONIOM QM/MM study

(2018) Henrique Silva Fernandes et al.   ACS Catalysis

Accelerating QM/MM Free Energy Computations via Intramolecular Force Matching

(2018) Phillip S. Hudson et al.   Journal of Chemical Theory and Computation

Accurate Estimation of Ligand Binding Affinity Changes upon Protein Mutation

(2018) Matteo Aldeghi et al.   ACS Central Science

Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations

(2017) Zoe Cournia et al.   Journal of Chemical Information and Modeling

Comparison of QM/MM Methods To Obtain Ligand-Binding Free Energies

(2017) Martin A. Olsson et al.   Journal of Chemical Theory and Computation

Computing converged free energy differences between levels of theory via nonequilibrium work methods: Challenges and opportunities

(2017) Fiona L. Kearns et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Convergence of single-step free energy perturbation

(2016) Stefan Boresch et al.   MOLECULAR PHYSICS

QM/MM free energy simulations: recent progress and challenges

(2016) Xiya Lu et al.   MOLECULAR SIMULATION

Unconstrained enhanced sampling for free energy calculations of biomolecules: a review

(2016) Yinglong Miao et al.   MOLECULAR SIMULATION

Principal component analysis: a review and recent developments

(2016) Ian T. Jolliffe et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Molecular dynamics simulations of large macromolecular complexes

(2015) Juan R Perilla et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Use of Nonequilibrium Work Methods to Compute Free Energy Differences Between Molecular Mechanical and Quantum Mechanical Representations of Molecular Systems

(2015) Phillip S. Hudson et al.   Journal of Physical Chemistry Letters

QM/MM through the 1990s: The First Twenty Years of Method Development and Applications

(2014) Meiyi Liu et al.   ISRAEL JOURNAL OF CHEMISTRY

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

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

Parametrization of DFTB3/3OB for Magnesium and Zinc for Chemical and Biological Applications

(2014) Xiya Lu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Computing Equilibrium Free Energies Using Non-Equilibrium Molecular Dynamics

(2013) Christoph Dellago et al.   Entropy

Eppur Si Muove! The 2013 Nobel Prize in Chemistry

(2013) Jeremy C. Smith et al.   STRUCTURE

Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

Enhanced Sampling in Free Energy Calculations: Combining SGLD with the Bennett’s Acceptance Ratio and Enveloping Distribution Sampling Methods

(2012) Gerhard König 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

Convergence of QM/MM free-energy perturbations based on molecular-mechanics or semiempirical simulations

(2012) Jimmy Heimdal et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

MSCALE: A General Utility for Multiscale Modeling

(2011) H. Lee Woodcock et al.   Journal of Chemical Theory and Computation

Good Practices in Free-Energy Calculations

(2010) Andrew Pohorille et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Optimum protocol for fast-switching free-energy calculations

(2010) Philipp Geiger et al.   PHYSICAL REVIEW E

Some recent techniques for free energy calculations

(2009) Eric Vanden-Eijnden   JOURNAL OF COMPUTATIONAL CHEMISTRY

Basic ingredients of free energy calculations: A review

(2009) Clara D. Christ et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Discovery Through the Computational Microscope

(2009) Eric H. Lee et al.   STRUCTURE

Computing the optimal protocol for finite-time processes in stochastic thermodynamics

(2008) Holger Then et al.   PHYSICAL REVIEW E