Free energies at QM accuracy from force fields via multimap targeted estimation
Published 2023 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Free energies at QM accuracy from force fields via multimap targeted estimation
Authors
Keywords
-
Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 120, Issue 46, Pages -
Publisher
Proceedings of the National Academy of Sciences
Online
2023-11-07
DOI
10.1073/pnas.2304308120
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- The Exascale Era is Upon Us: The Frontier supercomputer may be the first to reach 1,000,000,000,000,000,000 operations per second
- (2022) David Schneider IEEE SPECTRUM
- Assessing the Accuracy of Machine Learning Thermodynamic Perturbation Theory: Density Functional Theory and Beyond
- (2022) Basile Herzog et al. Journal of Chemical Theory and Computation
- Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches
- (2022) Phillip S. Hudson et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Optimizing the Calculation of Free Energy Differences in Nonequilibrium Work SQM/MM Switching Simulations
- (2022) Andreas Schöller et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Adaptive Monte Carlo augmented with normalizing flows
- (2022) Marylou Gabrié et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Multireference Generalization of the Weighted Thermodynamic Perturbation Method
- (2022) Timothy J. Giese et al. JOURNAL OF PHYSICAL CHEMISTRY A
- Skipping the Replica Exchange Ladder with Normalizing Flows
- (2022) Michele Invernizzi et al. Journal of Physical Chemistry Letters
- SAMPL7 Host–Guest Challenge Overview: assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations
- (2021) Martin Amezcua et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Targeted Free Energy Perturbation Revisited: Accurate Free Energies from Mapped Reference Potentials
- (2021) Andrea Rizzi et al. Journal of Physical Chemistry Letters
- D3R grand challenge 4: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies
- (2020) Conor D. Parks et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Thermodynamics of Transition Metal Ion Binding to Proteins
- (2020) Lin Frank Song et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Rethinking Metadynamics: From Bias Potentials to Probability Distributions
- (2020) Michele Invernizzi et al. Journal of Physical Chemistry Letters
- Ab initio calculations of free energy of activation at multiple electronic structure levels made affordable: An effective combination of perturbation theory and machine learning
- (2020) Tomas Bucko et al. Journal of Chemical Theory and Computation
- Large-Scale Assessment of Binding Free Energy Calculations in Active Drug Discovery Projects
- (2020) Christina E. M. Schindler et al. Journal of Chemical Information and Modeling
- Targeted free energy estimation via learned mappings
- (2020) Peter Wirnsberger et al. JOURNAL OF CHEMICAL PHYSICS
- Enhancing Water Sampling in Free Energy Calculations with Grand Canonical Monte Carlo
- (2020) Gregory A. Ross et al. Journal of Chemical Theory and Computation
- 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
- Host–Guest Relative Binding Affinities at Density-Functional Theory Level from Semiempirical Molecular Dynamics Simulations
- (2019) Meiting Wang et al. Journal of Chemical Theory and Computation
- Configurational mapping significantly increases the efficiency of solid-solid phase coexistence calculations via molecular dynamics: Determining the FCC-HCP coexistence line of Lennard-Jones particles
- (2019) Natalie P. Schieber et al. JOURNAL OF CHEMICAL PHYSICS
- 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
- Boltzmann generators: Sampling equilibrium states of many-body systems with deep learning
- (2019) Frank Noé et al. SCIENCE
- Computing RPA Adsorption Enthalpies by Machine Learning Thermodynamic Perturbation Theory
- (2019) Bilal Chehaibou et al. Journal of Chemical Theory and Computation
- Using reweighting and free energy surface interpolation to predict solid-solid phase diagrams
- (2018) Natalie P. Schieber et al. JOURNAL OF CHEMICAL PHYSICS
- Molecular Dynamics Simulations with Quantum Mechanics/Molecular Mechanics and Adaptive Neural Networks
- (2018) Lin Shen et al. Journal of Chemical Theory and Computation
- Relative Ligand-Binding Free Energies Calculated from Multiple Short QM/MM MD Simulations
- (2018) Casper Steinmann et al. Journal of Chemical Theory and Computation
- Metal–ligand interactions in drug design
- (2018) Laura Riccardi et al. Nature Reviews Chemistry
- Predicting Relative Binding Affinity Using Nonequilibrium QM/MM Simulations
- (2018) Meiting Wang et al. Journal of Chemical Theory and Computation
- 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
- Force matching as a stepping stone to QM/MM CB[8] host/guest binding free energies: a SAMPL6 cautionary tale
- (2018) Phillip S. Hudson et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- 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
- The atomic simulation environment—a Python library for working with atoms
- (2017) Ask Hjorth Larsen et al. JOURNAL OF PHYSICS-CONDENSED MATTER
- Comparison of Methods To Reweight from Classical Molecular Simulations to QM/MM Potentials
- (2016) Eric C. Dybeck et al. Journal of Chemical Theory and Computation
- Reformulation of Ensemble Averages via Coordinate Mapping
- (2016) Andrew J. Schultz et al. Journal of Chemical Theory and Computation
- Multiscale Quantum Mechanics/Molecular Mechanics Simulations with Neural Networks
- (2016) Lin Shen et al. Journal of Chemical Theory and Computation
- Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset
- (2016) Michael R. Shirts et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- How To Deal with Multiple Binding Poses in Alchemical Relative Protein–Ligand Binding Free Energy Calculations
- (2015) Joseph W. Kaus et al. Journal of Chemical Theory and Computation
- 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
- Very fast averaging of thermal properties of crystals by molecular simulation
- (2015) Sabry G. Moustafa et al. PHYSICAL REVIEW E
- 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
- PLUMED 2: New feathers for an old bird
- (2013) Gareth A. Tribello et al. COMPUTER PHYSICS COMMUNICATIONS
- Multistate reweighting and configuration mapping together accelerate the efficiency of thermodynamic calculations as a function of molecular geometry by orders of magnitude
- (2013) Himanshu Paliwal et al. JOURNAL OF CHEMICAL PHYSICS
- Parametrization and Benchmark of DFTB3 for Organic Molecules
- (2012) Michael Gaus et al. Journal of Chemical Theory and Computation
- On achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinities
- (2012) L. Wang et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- 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
- Efficient calculation of temperature dependence of solid-phase free energies by overlap sampling coupled with harmonically targeted perturbation
- (2010) Tai Boon Tan et al. JOURNAL OF CHEMICAL PHYSICS
- Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics
- (2009) M. Bonomi et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields
- (2009) K. Vanommeslaeghe et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- CHARMM: The biomolecular simulation program
- (2009) B. R. Brooks et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Using bijective maps to improve free-energy estimates
- (2009) A. M. Hahn et al. PHYSICAL REVIEW E
- Statistically optimal analysis of samples from multiple equilibrium states
- (2008) Michael R. Shirts et al. JOURNAL OF CHEMICAL PHYSICS
- Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
- (2008) Alessandro Barducci et al. PHYSICAL REVIEW LETTERS
Add your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload NowAsk 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