Graph neural network approaches for drug-target interactions

Z Zhang, L Chen, F Zhong, D Wang, J Jiang… - Current Opinion in …, 2022 - Elsevier
Developing new drugs remains prohibitively expensive, time-consuming, and often involves
safety issues. Accurate prediction of drug-target interactions (DTIs) can guide the drug …

Deep learning in virtual screening: recent applications and developments

TB Kimber, Y Chen, A Volkamer - International journal of molecular …, 2021 - mdpi.com
Drug discovery is a cost and time-intensive process that is often assisted by computational
methods, such as virtual screening, to speed up and guide the design of new compounds …

[HTML][HTML] Deep learning methods in protein structure prediction

M Torrisi, G Pollastri, Q Le - Computational and Structural Biotechnology …, 2020 - Elsevier
Abstract Protein Structure Prediction is a central topic in Structural Bioinformatics. Since
the'60s statistical methods, followed by increasingly complex Machine Learning and recently …

Drug–target affinity prediction using graph neural network and contact maps

M Jiang, Z Li, S Zhang, S Wang, X Wang, Q Yuan… - RSC …, 2020 - pubs.rsc.org
Computer-aided drug design uses high-performance computers to simulate the tasks in drug
design, which is a promising research area. Drug–target affinity (DTA) prediction is the most …

Protein tertiary structure modeling driven by deep learning and contact distance prediction in CASP13

J Hou, T Wu, R Cao, J Cheng - Proteins: Structure, Function …, 2019 - Wiley Online Library
Predicting residue‐residue distance relationships (eg, contacts) has become the key
direction to advance protein structure prediction since 2014 CASP11 experiment, while …

Deep learning-based advances in protein structure prediction

SC Pakhrin, B Shrestha, B Adhikari, DB Kc - International journal of …, 2021 - mdpi.com
Obtaining an accurate description of protein structure is a fundamental step toward
understanding the underpinning of biology. Although recent advances in experimental …

Protein structure prediction: conventional and deep learning perspectives

VA Jisna, PB Jayaraj - The protein journal, 2021 - Springer
Protein structure prediction is a way to bridge the sequence-structure gap, one of the main
challenges in computational biology and chemistry. Predicting any protein's accurate …

Compound–protein interaction prediction by deep learning: databases, descriptors and models

BX Du, Y Qin, YF Jiang, Y Xu, SM Yiu, H Yu, JY Shi - Drug discovery today, 2022 - Elsevier
The screening of compound–protein interactions (CPIs) is one of the most crucial steps in
finding hit and lead compounds. Deep learning (DL) methods for CPI prediction can address …

NHGNN-DTA: a node-adaptive hybrid graph neural network for interpretable drug–target binding affinity prediction

H He, G Chen, CYC Chen - Bioinformatics, 2023 - academic.oup.com
Motivation Large-scale prediction of drug–target affinity (DTA) plays an important role in
drug discovery. In recent years, machine learning algorithms have made great progress in …

Hierarchical graph representation learning for the prediction of drug-target binding affinity

Z Chu, F Huang, H Fu, Y Quan, X Zhou, S Liu… - Information …, 2022 - Elsevier
Computationally predicting drug-target binding affinity (DTA) has attracted increasing
attention due to its benefit for accelerating drug discovery. Currently, numerous deep …