Protein–ligand scoring with convolutional neural networks
Computational approaches to drug discovery can reduce the time and cost associated with
experimental assays and enable the screening of novel chemotypes. Structure-based drug …
experimental assays and enable the screening of novel chemotypes. Structure-based drug …
Three-dimensional convolutional neural networks and a cross-docked data set for structure-based drug design
PG Francoeur, T Masuda, J Sunseri, A Jia… - Journal of chemical …, 2020 - ACS Publications
One of the main challenges in drug discovery is predicting protein–ligand binding affinity.
Recently, machine learning approaches have made substantial progress on this task …
Recently, machine learning approaches have made substantial progress on this task …
Visualizing convolutional neural network protein-ligand scoring
Protein-ligand scoring is an important step in a structure-based drug design pipeline.
Selecting a correct binding pose and predicting the binding affinity of a protein-ligand …
Selecting a correct binding pose and predicting the binding affinity of a protein-ligand …
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 …
Improving protein–ligand docking and screening accuracies by incorporating a scoring function correction term
Scoring functions are important components in molecular docking for structure-based drug
discovery. Traditional scoring functions, generally empirical-or force field-based, are robust …
discovery. Traditional scoring functions, generally empirical-or force field-based, are robust …
Beware of Machine Learning-Based Scoring Functions On the Danger of Developing Black Boxes
Training machine learning algorithms with protein–ligand descriptors has recently gained
considerable attention to predict binding constants from atomic coordinates. Starting from a …
considerable attention to predict binding constants from atomic coordinates. Starting from a …
Graph convolutional neural networks for predicting drug-target interactions
Accurate determination of target-ligand interactions is crucial in the drug discovery process.
In this paper, we propose a graph-convolutional (Graph-CNN) framework for predicting …
In this paper, we propose a graph-convolutional (Graph-CNN) framework for predicting …
Improved protein–ligand binding affinity prediction with structure-based deep fusion inference
Predicting accurate protein–ligand binding affinities is an important task in drug discovery
but remains a challenge even with computationally expensive biophysics-based energy …
but remains a challenge even with computationally expensive biophysics-based energy …
Convolutional neural network scoring and minimization in the D3R 2017 community challenge
We assess the ability of our convolutional neural network (CNN)-based scoring functions to
perform several common tasks in the domain of drug discovery. These include correctly …
perform several common tasks in the domain of drug discovery. These include correctly …
Evaluation of AutoDock and AutoDock Vina on the CASF-2013 benchmark
T Gaillard - Journal of chemical information and modeling, 2018 - ACS Publications
Computer-aided protein–ligand binding predictions are a valuable help in drug discovery.
Protein–ligand docking programs generally consist of two main components: a scoring …
Protein–ligand docking programs generally consist of two main components: a scoring …