[HTML][HTML] Best practices for alchemical free energy calculations [article v1. 0]
Alchemical free energy calculations are a useful tool for predicting free energy differences
associated with the transfer of molecules from one environment to another. The hallmark of …
associated with the transfer of molecules from one environment to another. The hallmark of …
Alchemical binding free energy calculations in AMBER20: Advances and best practices for drug discovery
Predicting protein–ligand binding affinities and the associated thermodynamics of
biomolecular recognition is a primary objective of structure-based drug design. Alchemical …
biomolecular recognition is a primary objective of structure-based drug design. Alchemical …
Development of a robust indirect approach for MM→ QM free energy calculations that combines force-matched reference potential and Bennett's acceptance ratio …
TJ Giese, DM York - Journal of chemical theory and computation, 2019 - ACS Publications
We use the PBE0/6-31G* density functional method to perform ab initio quantum
mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations under …
mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations under …
Perspective: Reference-Potential Methods for the Study of Thermodynamic Properties in Chemical Processes: Theory, Applications, and Pitfalls
In silico investigations of enzymatic reactions and chemical reactions in condensed phases
often suffer from formidable computational costs due to a large number of degrees of …
often suffer from formidable computational costs due to a large number of degrees of …
Computing converged free energy differences between levels of theory via nonequilibrium work methods: Challenges and opportunities
We demonstrate that Jarzynski's equation can be used to reliably compute free energy
differences between low and high level representations of systems. The need for such a …
differences between low and high level representations of systems. The need for such a …
Absolute proton hydration free energy, surface potential of water, and redox potential of the hydrogen electrode from first principles: QM/MM MD free-energy …
TS Hofer, PH Hünenberger - The Journal of chemical physics, 2018 - pubs.aip.org
Absolute proton hydration free energy, surface potential of water, and redox potential of the
hydrogen electrode from first principles: QM/MM MD free-energy simulations of sodium and …
hydrogen electrode from first principles: QM/MM MD free-energy simulations of sodium and …
Accurate machine learning force fields via experimental and simulation data fusion
Abstract Machine Learning (ML)-based force fields are attracting ever-increasing interest
due to their capacity to span spatiotemporal scales of classical interatomic potentials at …
due to their capacity to span spatiotemporal scales of classical interatomic potentials at …
Targeted free energy perturbation revisited: Accurate free energies from mapped reference potentials
We present an approach that extends the theory of targeted free energy perturbation (TFEP)
to calculate free energy differences and free energy surfaces at an accurate quantum …
to calculate free energy differences and free energy surfaces at an accurate quantum …
Free energies at QM accuracy from force fields via multimap targeted estimation
Accurate predictions of ligand binding affinities would greatly accelerate the first stages of
drug discovery campaigns. However, using highly accurate interatomic potentials based on …
drug discovery campaigns. However, using highly accurate interatomic potentials based on …
Accurate and Efficient Multilevel Free Energy Simulations with Neural Network-Assisted Enhanced Sampling
Free energy differences (Δ F) are essential to quantitative characterization and
understanding of chemical and biological processes. Their direct estimation with an …
understanding of chemical and biological processes. Their direct estimation with an …