Modern alchemical free energy methods for drug discovery explained
DM York - ACS Physical Chemistry Au, 2023 - ACS Publications
This Perspective provides a contextual explanation of the current state-of-the-art alchemical
free energy methods and their role in drug discovery as well as highlights select emerging …
free energy methods and their role in drug discovery as well as highlights select emerging …
Comparison of receptor–ligand restraint schemes for alchemical absolute binding free energy calculations
Alchemical absolute binding free energy calculations are of increasing interest in drug
discovery. These calculations require restraints between the receptor and ligand to restrict …
discovery. These calculations require restraints between the receptor and ligand to restrict …
Current State of Open Source Force Fields in Protein–Ligand Binding Affinity Predictions
In drug discovery, the in silico prediction of binding affinity is one of the major means to
prioritize compounds for synthesis. Alchemical relative binding free energy (RBFE) …
prioritize compounds for synthesis. Alchemical relative binding free energy (RBFE) …
Alchemical Enhanced Sampling with Optimized Phase Space Overlap
An alchemical enhanced sampling (ACES) method has recently been introduced to facilitate
importance sampling in free energy simulations. The method achieves enhanced sampling …
importance sampling in free energy simulations. The method achieves enhanced sampling …
Validation of the Alchemical Transfer Method for the Estimation of Relative Binding Affinities of Molecular Series
F Sabanés Zariquiey, A Pérez… - Journal of chemical …, 2023 - ACS Publications
The accurate prediction of protein–ligand binding affinities is crucial for drug discovery.
Alchemical free energy calculations have become a popular tool for this purpose. However …
Alchemical free energy calculations have become a popular tool for this purpose. However …
Automated Adaptive Absolute Binding Free Energy Calculations
Alchemical absolute binding free energy (ABFE) calculations have substantial potential in
drug discovery, but are often prohibitively computationally expensive. To unlock their …
drug discovery, but are often prohibitively computationally expensive. To unlock their …
Kartograf: A Geometrically Accurate Atom Mapper for Hybrid-Topology Relative Free Energy Calculations
Relative binding free energy (RBFE) calculations have emerged as a powerful tool that
supports ligand optimization in drug discovery. Despite many successes, the use of RBFEs …
supports ligand optimization in drug discovery. Despite many successes, the use of RBFEs …
PopShift: A thermodynamically sound approach to estimate binding free energies by accounting for ligand-induced population shifts from a ligand-free MSM
LG Smith, B Novak, M Osato, DL Mobley… - Biophysical Journal, 2024 - cell.com
1Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA,
USA, 2Department of Biochemistry and Biophysics, Washington University in St. Louis, St …
USA, 2Department of Biochemistry and Biophysics, Washington University in St. Louis, St …
Accelerating and Automating the Free Energy Perturbation Absolute Binding Free Energy Calculation with the RED-E Function
R Liu, W Li, Y Yao, Y Wu, HB Luo… - Journal of Chemical …, 2023 - ACS Publications
The accurate prediction of the binding affinities between small molecules and biological
macromolecules plays a fundamental role in structure-based drug design, which is still …
macromolecules plays a fundamental role in structure-based drug design, which is still …
Improvements in Precision of Relative Binding Free Energy Calculations Afforded by the Alchemical Enhanced Sampling (ACES) Approach
HC Tsai, J Xu, Z Guo, Y Yi, C Tian, X Que… - Journal of Chemical …, 2024 - ACS Publications
Accurate in silico predictions of how strongly small molecules bind to proteins, such as those
afforded by relative binding free energy (RBFE) calculations, can greatly increase the …
afforded by relative binding free energy (RBFE) calculations, can greatly increase the …