Relative binding free energy calculations in drug discovery: recent advances and practical considerations
Accurate in silico prediction of protein–ligand binding affinities has been a primary objective
of structure-based drug design for decades due to the putative value it would bring to the …
of structure-based drug design for decades due to the putative value it would bring to the …
An overview of molecular modeling for drug discovery with specific illustrative examples of applications
In this paper we review the current status of high-performance computing applications in the
general area of drug discovery. We provide an introduction to the methodologies applied at …
general area of drug discovery. We provide an introduction to the methodologies applied at …
KDEEP: Protein–Ligand Absolute Binding Affinity Prediction via 3D-Convolutional Neural Networks
Accurately predicting protein–ligand binding affinities is an important problem in
computational chemistry since it can substantially accelerate drug discovery for virtual …
computational chemistry since it can substantially accelerate drug discovery for virtual …
[HTML][HTML] Best practices for alchemical free energy calculations [article v1. 0]
Alchemical free energy calculations are a useful tool for predicting free energy differences
associated with the transfer of molecules from one environment to another. The hallmark of …
associated with the transfer of molecules from one environment to another. The hallmark of …
Large scale relative protein ligand binding affinities using non-equilibrium alchemy
Ligand binding affinity calculations based on molecular dynamics (MD) simulations and non-
physical (alchemical) thermodynamic cycles have shown great promise for structure-based …
physical (alchemical) thermodynamic cycles have shown great promise for structure-based …
Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches
Entropy effects play an important role in drug–target interactions, but the entropic
contribution to ligand-binding affinity is often neglected by end-point binding free energy …
contribution to ligand-binding affinity is often neglected by end-point binding free energy …
D3R Grand Challenge 2: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies
Abstract The Drug Design Data Resource (D3R) ran Grand Challenge 2 (GC2) from
September 2016 through February 2017. This challenge was based on a dataset of …
September 2016 through February 2017. This challenge was based on a dataset of …
Alchemical absolute protein–ligand binding free energies for drug design
The recent advances in relative protein–ligand binding free energy calculations have shown
the value of alchemical methods in drug discovery. Accurately assessing absolute binding …
the value of alchemical methods in drug discovery. Accurately assessing absolute binding …
Evolution of alchemical free energy methods in drug discovery
The goal of the present manuscript is to succinctly trace the key technological steps in the
evolution of alchemical free energy methods (AFEMs) from a purely theoretical construct to a …
evolution of alchemical free energy methods (AFEMs) from a purely theoretical construct to a …
The maximal and current accuracy of rigorous protein-ligand binding free energy calculations
Computational techniques can speed up the identification of hits and accelerate the
development of candidate molecules for drug discovery. Among techniques for predicting …
development of candidate molecules for drug discovery. Among techniques for predicting …