Artificial intelligence in the prediction of protein–ligand interactions: recent advances and future directions

A Dhakal, C McKay, JJ Tanner… - Briefings in …, 2022 - academic.oup.com
New drug production, from target identification to marketing approval, takes over 12 years
and can cost around $2.6 billion. Furthermore, the COVID-19 pandemic has unveiled the …

Application advances of deep learning methods for de novo drug design and molecular dynamics simulation

Q Bai, S Liu, Y Tian, T Xu… - Wiley …, 2022 - Wiley Online Library
De novo drug design is a stationary way to build novel ligands in the confined pocket of
receptor by assembling the atoms or fragments, while molecular dynamics (MD) simulation …

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 …

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 …

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 …

BACPI: a bi-directional attention neural network for compound–protein interaction and binding affinity prediction

M Li, Z Lu, Y Wu, YH Li - Bioinformatics, 2022 - academic.oup.com
Motivation The identification of compound–protein interactions (CPIs) is an essential step in
the process of drug discovery. The experimental determination of CPIs is known for a large …

CAPLA: improved prediction of protein–ligand binding affinity by a deep learning approach based on a cross-attention mechanism

Z Jin, T Wu, T Chen, D Pan, X Wang, J Xie… - …, 2023 - academic.oup.com
Motivation Accurate and rapid prediction of protein–ligand binding affinity is a great
challenge currently encountered in drug discovery. Recent advances have manifested a …

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 …

[HTML][HTML] DTITR: End-to-end drug–target binding affinity prediction with transformers

NRC Monteiro, JL Oliveira, JP Arrais - Computers in Biology and Medicine, 2022 - Elsevier
The accurate identification of Drug–Target Interactions (DTIs) remains a critical turning point
in drug discovery and understanding of the binding process. Despite recent advances 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 …