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Performance and analysis of the alchemical transfer method for binding-free-energy predictions of diverse ligands
The Alchemical Transfer Method (ATM) is herein validated against the relative binding-free
energies (RBFEs) of a diverse set of protein–ligand complexes. We employed a streamlined …
energies (RBFEs) of a diverse set of protein–ligand complexes. We employed a streamlined …
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 …
Pandemic drugs at pandemic speed: infrastructure for accelerating COVID-19 drug discovery with hybrid machine learning-and physics-based simulations on high …
The race to meet the challenges of the global pandemic has served as a reminder that the
existing drug discovery process is expensive, inefficient and slow. There is a major …
existing drug discovery process is expensive, inefficient and slow. There is a major …
Large scale study of ligand–protein relative binding free energy calculations: actionable predictions from statistically robust protocols
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 …
Validation of the alchemical transfer method for the estimation of relative binding affinities of molecular series
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 …
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 …
What to Make of Zero: Resolving the Statistical Noise from Conformational Reorganization in Alchemical Binding Free Energy Estimates with Metadynamics Sampling
We introduce the self-relative binding free energy (self-RBFE) approach to evaluate the
intrinsic statistical variance of dual-topology alchemical binding free energy estimators. The …
intrinsic statistical variance of dual-topology alchemical binding free energy estimators. The …
Ensemble simulations and experimental free energy distributions: Evaluation and characterization of isoxazole amides as SMYD3 inhibitors
Optimization of binding affinities for ligands to their target protein is a primary objective in
rational drug discovery. Herein, we report on a collaborative study that evaluates various …
rational drug discovery. Herein, we report on a collaborative study that evaluates various …
The effect of protein mutations on drug binding suggests ensuing personalised drug selection
The advent of personalised medicine promises a deeper understanding of mechanisms and
therefore therapies. However, the connection between genomic sequences and clinical …
therefore therapies. However, the connection between genomic sequences and clinical …