Comparison of Equilibrium and Nonequilibrium Approaches for Relative Binding Free Energy Predictions
Alchemical relative binding free energy calculations have recently found important
applications in drug optimization. A series of congeneric compounds are generated from a …
applications in drug optimization. A series of congeneric compounds are generated from a …
Large scale study of ligand–protein relative binding free energy calculations: actionable predictions from statistically robust protocols
AP Bhati, PV Coveney - Journal of Chemical Theory and …, 2022 - ACS Publications
The accurate and reliable prediction of protein–ligand binding affinities can play a central
role in the drug discovery process as well as in personalized medicine. Of considerable …
role in the drug discovery process as well as in personalized medicine. Of considerable …
Ensemble-Based Approaches Ensure Reliability and Reproducibility
It is increasingly widely recognized that ensemble-based approaches are required to
achieve reliability, accuracy, and precision in molecular dynamics calculations. The purpose …
achieve reliability, accuracy, and precision in molecular dynamics calculations. The purpose …
Optimal Molecular Design: Generative Active Learning Combining REINVENT with Precise Binding Free Energy Ranking Simulations
Active learning (AL) is a specific instance of sequential experimental design and uses
machine learning to intelligently choose the next data point or batch of molecular structures …
machine learning to intelligently choose the next data point or batch of molecular structures …
Integration of molecular coarse-grained model into geometric representation learning framework for protein-protein complex property prediction
Abstract Structure-based machine learning algorithms have been utilized to predict the
properties of protein-protein interaction (PPI) complexes, such as binding affinity, which is …
properties of protein-protein interaction (PPI) complexes, such as binding affinity, which is …
Long Time Scale Ensemble Methods in Molecular Dynamics: Ligand–Protein Interactions and Allostery in SARS-CoV-2 Targets
We subject a series of five protein–ligand systems which contain important SARS-CoV-2
targets, 3-chymotrypsin-like protease (3CLPro), papain-like protease, and adenosine ribose …
targets, 3-chymotrypsin-like protease (3CLPro), papain-like protease, and adenosine ribose …
Equilibrium and Nonequilibrium Ensemble Methods for Accurate, Precise and Reproducible Absolute Binding Free Energy Calculations
Free energy calculations for protein–ligand complexes have become widespread in recent
years owing to several conceptual, methodological and technological advances. Central …
years owing to several conceptual, methodological and technological advances. Central …
Alchemical free energy estimators and molecular dynamics engines: accuracy, precision, and reproducibility
The binding free energy between a ligand and its target protein is an essential quantity to
know at all stages of the drug discovery pipeline. Assessing this value computationally can …
know at all stages of the drug discovery pipeline. Assessing this value computationally can …
Meta-Learning Enables Complex Cluster-Specific Few-Shot Binding Affinity Prediction for Protein–Protein Interactions
Predicting protein–protein interaction (PPI) binding affinities in unseen protein complex
clusters is essential for elucidating complex protein interactions and for the targeted …
clusters is essential for elucidating complex protein interactions and for the targeted …
The performance of ensemble-based free energy protocols in computing binding affinities to ROS1 kinase
Optimization of binding affinities for compounds to their target protein is a primary objective
in drug discovery. Herein we report on a collaborative study that evaluates a set of …
in drug discovery. Herein we report on a collaborative study that evaluates a set of …