Deepbindgcn: Integrating molecular vector representation with graph convolutional neural networks for protein–ligand interaction prediction

H Zhang, KM Saravanan, JZH Zhang - Molecules, 2023 - mdpi.com
The core of large-scale drug virtual screening is to select the binders accurately and
efficiently with high affinity from large libraries of small molecules in which non-binders are …

[HTML][HTML] Predicting or pretending: artificial intelligence for protein-ligand interactions lack of sufficiently large and unbiased datasets

J Yang, C Shen, N Huang - Frontiers in pharmacology, 2020 - frontiersin.org
Predicting protein-ligand interactions using artificial intelligence (AI) models has attracted
great interest in recent years. However, data-driven AI models unequivocally suffer from a …

GraphscoreDTA: optimized graph neural network for protein–ligand binding affinity prediction

K Wang, R Zhou, J Tang, M Li - Bioinformatics, 2023 - academic.oup.com
Motivation Computational approaches for identifying the protein–ligand binding affinity can
greatly facilitate drug discovery and development. At present, many deep learning-based …

graphDelta: MPNN scoring function for the affinity prediction of protein–ligand complexes

DS Karlov, S Sosnin, MV Fedorov, P Popov - ACS omega, 2020 - ACS Publications
In this work, we present graph-convolutional neural networks for the prediction of binding
constants of protein–ligand complexes. We derived the model using multi task learning …

Hac-net: A hybrid attention-based convolutional neural network for highly accurate protein–ligand binding affinity prediction

GW Kyro, RI Brent, VS Batista - Journal of Chemical Information …, 2023 - ACS Publications
Applying deep learning concepts from image detection and graph theory has greatly
advanced protein–ligand binding affinity prediction, a challenge with enormous ramifications …

Sfcnn: a novel scoring function based on 3D convolutional neural network for accurate and stable protein–ligand affinity prediction

Y Wang, Z Wei, L Xi - BMC bioinformatics, 2022 - Springer
Background Computer-aided drug design provides an effective method of identifying lead
compounds. However, success rates are significantly bottlenecked by the lack of accurate …

Effects of data quality and quantity on deep learning for protein-ligand binding affinity prediction

FJ Fan, Y Shi - Bioorganic & Medicinal Chemistry, 2022 - Elsevier
Prediction of protein-ligand binding affinities is crucial for computational drug discovery. A
number of deep learning approaches have been developed in recent years to improve the …

DeepCDA: deep cross-domain compound–protein affinity prediction through LSTM and convolutional neural networks

K Abbasi, P Razzaghi, A Poso, M Amanlou… - …, 2020 - academic.oup.com
Motivation An essential part of drug discovery is the accurate prediction of the binding affinity
of new compound–protein pairs. Most of the standard computational methods assume that …

KDEEP: Protein–Ligand Absolute Binding Affinity Prediction via 3D-Convolutional Neural Networks

J Jiménez, M Skalic, G Martinez-Rosell… - Journal of chemical …, 2018 - ACS Publications
Accurately predicting protein–ligand binding affinities is an important problem in
computational chemistry since it can substantially accelerate drug discovery for virtual …

Planet: a multi-objective graph neural network model for protein–ligand binding affinity prediction

X Zhang, H Gao, H Wang, Z Chen… - Journal of Chemical …, 2023 - ACS Publications
Predicting protein–ligand binding affinity is a central issue in drug design. Various deep
learning models have been published in recent years, where many of them rely on 3D …