Neural multi-task learning in drug design

S Allenspach, JA Hiss, G Schneider - Nature Machine Intelligence, 2024 - nature.com
Multi-task learning (MTL) is a machine learning paradigm that aims to enhance the
generalization of predictive models by leveraging shared information across multiple tasks …

Structure‐Based Drug Discovery with Deep Learning

R Özçelik, D van Tilborg, J Jiménez‐Luna… - …, 2023 - Wiley Online Library
Artificial intelligence (AI) in the form of deep learning has promise for drug discovery and
chemical biology, for example, to predict protein structure and molecular bioactivity, plan …

Interpretable bilinear attention network with domain adaptation improves drug–target prediction

P Bai, F Miljković, B John, H Lu - Nature Machine Intelligence, 2023 - nature.com
Predicting drug–target interaction is key for drug discovery. Recent deep learning-based
methods show promising performance, but two challenges remain: how to explicitly model …

[HTML][HTML] DeepPROTACs is a deep learning-based targeted degradation predictor for PROTACs

F Li, Q Hu, X Zhang, R Sun, Z Liu, S Wu, S Tian… - Nature …, 2022 - nature.com
The rational design of PROTACs is difficult due to their obscure structure-activity
relationship. This study introduces a deep neural network model-DeepPROTACs to help …

HyperAttentionDTI: improving drug–protein interaction prediction by sequence-based deep learning with attention mechanism

Q Zhao, H Zhao, K Zheng, J Wang - Bioinformatics, 2022 - academic.oup.com
Motivation Identifying drug–target interactions (DTIs) is a crucial step in drug repurposing
and drug discovery. Accurately identifying DTIs in silico can significantly shorten …

Geometric interaction graph neural network for predicting protein–ligand binding affinities from 3d structures (gign)

Z Yang, W Zhong, Q Lv, T Dong… - The journal of physical …, 2023 - ACS Publications
Predicting protein–ligand binding affinities (PLAs) is a core problem in drug discovery.
Recent advances have shown great potential in applying machine learning (ML) for PLA …

FusionDTA: attention-based feature polymerizer and knowledge distillation for drug-target binding affinity prediction

W Yuan, G Chen, CYC Chen - Briefings in Bioinformatics, 2022 - academic.oup.com
The prediction of drug-target affinity (DTA) plays an increasingly important role in drug
discovery. Nowadays, lots of prediction methods focus on feature encoding of drugs and …

[HTML][HTML] Affinity2Vec: drug-target binding affinity prediction through representation learning, graph mining, and machine learning

MA Thafar, M Alshahrani, S Albaradei, T Gojobori… - Scientific reports, 2022 - nature.com
Drug-target interaction (DTI) prediction plays a crucial role in drug repositioning and virtual
drug screening. Most DTI prediction methods cast the problem as a binary classification task …

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 …

Predicting drug–target binding affinity through molecule representation block based on multi-head attention and skip connection

L Zhang, CC Wang, X Chen - Briefings in Bioinformatics, 2022 - academic.oup.com
Exiting computational models for drug–target binding affinity prediction have much room for
improvement in prediction accuracy, robustness and generalization ability. Most deep …