Recent Advances in Alchemical Binding Free Energy Calculations for Drug Discovery

AMBER Free Energy Tools: A New Framework for the Design of Optimized Alchemical Transformation Pathways

(2023) Hsu-Chun Tsai et al.   Journal of Chemical Theory and Computation

Pre-Exascale Computing of Protein–Ligand Binding Free Energies with Open Source Software for Drug Design

(2022) Vytautas Gapsys et al.   Journal of Chemical Information and Modeling

Fast and Effective Prediction of the Absolute Binding Free Energies of Covalent Inhibitors of SARS-CoV-2 Main Protease and 20S Proteasome

(2022) Jiao Zhou et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

How does a small molecule bind at a cryptic binding site?

(2022) Yibing Shan et al.   PLoS Computational Biology

Induced-Fit Docking Enables Accurate Free Energy Perturbation Calculations in Homology Models

(2022) Tianchuan Xu et al.   Journal of Chemical Theory and Computation

Absolute binding free energy calculations improve enrichment of actives in virtual compound screening

(2022) Mudong Feng et al.   Scientific Reports

In Silico Positional Analogue Scanning with Amber GPU-TI

(2022) Yuan Hu et al.   Journal of Chemical Information and Modeling

Are Deep Learning Structural Models Sufficiently Accurate for Free-Energy Calculations? Application of FEP+ to AlphaFold2-Predicted Structures

(2022) Thijs Beuming et al.   Journal of Chemical Information and Modeling

Investigating the Dynamic Binding Behavior of PMX53 Cooperating with Allosteric Antagonist NDT9513727 to C5a Anaphylatoxin Chemotactic Receptor 1 through Gaussian Accelerated Molecular Dynamics and Free-Energy Perturbation Simulations

(2022) An Xiaoli et al.   ACS Chemical Neuroscience

Free Energy Perturbation in the Design of EED Ligands as Inhibitors of Polycomb Repressive Complex 2 (PRC2) Methyltransferase

(2021) Daniel H. O' Donovan et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Holistic drug design for multiparameter optimization in modern small molecule drug discovery

(2021) Lewis D. Pennington et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Predicting the Relative Binding Affinity for Reversible Covalent Inhibitors by Free Energy Perturbation Calculations

(2021) Vinícius Bonatto et al.   Journal of Chemical Information and Modeling

Free energy perturbation (FEP)-guided scaffold hopping

(2021) Deyan Wu et al.   Acta Pharmaceutica Sinica B

Impact of Different Automated Binding Pose Generation Approaches on Relative Binding Free Energy Simulations

(2020) Daniel Cappel et al.   Journal of Chemical Information and Modeling

Positional Analogue Scanning: An Effective Strategy for Multiparameter Optimization in Drug Design

(2020) Lewis D. Pennington et al.   JOURNAL OF MEDICINAL CHEMISTRY

Impact of Protein Preparation on Resulting Accuracy of FEP Calculations

(2020) Amy Y. Shih et al.   Journal of Chemical Information and Modeling

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

Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery

(2020) Tai-Sung Lee et al.   Journal of Chemical Information and Modeling

Evolution of Alchemical Free Energy Methods in Drug Discovery

(2020) Lin Frank Song et al.   Journal of Chemical Information and Modeling

Affinity and Selectivity Assessment of Covalent Inhibitors by Free Energy Calculations

(2020) Levente M. Mihalovits et al.   Journal of Chemical Information and Modeling

General Theory of Fragment Linking in Molecular Design: Why Fragment Linking Rarely Succeeds and How to Improve Outcomes

(2020) Haoyu S. Yu et al.   Journal of Chemical Theory and Computation

3,4-Dihydropyrimidin-2(1H)-ones as Antagonists of the Human A2B Adenosine Receptor: Optimization, Structure–Activity Relationship Studies, and Enantiospecific Recognition

(2020) María Majellaro et al.   JOURNAL OF MEDICINAL CHEMISTRY

Ranking Reversible Covalent Drugs: From Free Energy Perturbation to Fragment Docking

(2019) Han Zhang et al.   Journal of Chemical Information and Modeling

Toward Atomistic Modeling of Irreversible Covalent Inhibitor Binding Kinetics

(2019) Haoyu S. Yu et al.   Journal of Chemical Information and Modeling

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

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

Accurate Binding Free Energy Predictions in Fragment Optimization

(2015) Thomas B. Steinbrecher et al.   Journal of Chemical Information and Modeling

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

Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

(2015) Lingle Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY