Machine Learning for Sequence and Structure-Based Protein–Ligand Interaction Prediction

Y Zhang, S Li, K Meng, S Sun - Journal of Chemical Information …, 2024 - ACS Publications
Developing new drugs is too expensive and time-consuming. Accurately predicting the
interaction between drugs and targets will likely change how the drug is discovered …

Deciphering the lexicon of protein targets: a review on multifaceted drug discovery in the era of artificial intelligence

S Nandi, S Bhaduri, D Das, P Ghosh… - Molecular …, 2024 - ACS Publications
Understanding protein sequence and structure is essential for understanding protein–
protein interactions (PPIs), which are essential for many biological processes and diseases …

Hydrascreen: A generalizable structure-based deep learning approach to drug discovery

A Prat, H Abdel Aty, O Bastas… - Journal of Chemical …, 2023 - ACS Publications
We propose HydraScreen, a deep-learning framework for safe and robust accelerated drug
discovery. HydraScreen utilizes a state-of-the-art 3D convolutional neural network designed …

[HTML][HTML] The Impact of Data on Structure-Based Binding Affinity Predictions Using Deep Neural Networks

PY Libouban, S Aci-Sèche, JC Gómez-Tamayo… - International Journal of …, 2023 - mdpi.com
Artificial intelligence (AI) has gained significant traction in the field of drug discovery, with
deep learning (DL) algorithms playing a crucial role in predicting protein–ligand binding …

Directional ΔG Neural Network (DrΔG-Net): A Modular Neural Network Approach to Binding Free Energy Prediction

DP Metcalf, ZL Glick, A Bortolato, A Jiang… - Journal of Chemical …, 2024 - ACS Publications
The protein–ligand binding free energy is a central quantity in structure-based
computational drug discovery efforts. Although popular alchemical methods provide sound …

Multi-task bioassay pre-training for protein-ligand binding affinity prediction

J Yan, Z Ye, Z Yang, C Lu, S Zhang… - Briefings in …, 2024 - academic.oup.com
Protein–ligand binding affinity (PLBA) prediction is the fundamental task in drug discovery.
Recently, various deep learning-based models predict binding affinity by incorporating the …

GraphLambda: fusion graph neural networks for binding affinity prediction

G Mqawass, P Popov - Journal of Chemical Information and …, 2024 - ACS Publications
Predicting the binding affinity of protein–ligand complexes is crucial for computer-aided drug
discovery (CADD) and the identification of potential drug candidates. The deep learning …

Toward generalizable structure‐based deep learning models for protein–ligand interaction prediction: Challenges and strategies

S Moon, W Zhung, WY Kim - Wiley Interdisciplinary Reviews …, 2024 - Wiley Online Library
Accurate and rapid prediction of protein–ligand interactions (PLIs) is the fundamental
challenge of drug discovery. Deep learning methods have been harnessed for this purpose …

Modern machine‐learning for binding affinity estimation of protein–ligand complexes: Progress, opportunities, and challenges

T Harren, T Gutermuth, C Grebner… - Wiley …, 2024 - Wiley Online Library
Abstract Structure‐based drug design is a widely applied approach in the discovery of new
lead compounds for known therapeutic targets. In most structure‐based drug design …

[HTML][HTML] From GPUs to AI and quantum: three waves of acceleration in bioinformatics

B Schmidt, A Hildebrandt - Drug Discovery Today, 2024 - Elsevier
The enormous growth in the amount of data generated by the life sciences is continuously
shifting the field from model-driven science towards data-driven science. The need for …