Decoding the protein–ligand interactions using parallel graph neural networks

C Knutson, M Bontha, JA Bilbrey, N Kumar - Scientific reports, 2022 - nature.com
Protein–ligand interactions (PLIs) are essential for biochemical functionality and their
identification is crucial for estimating biophysical properties for rational therapeutic design …

Ssnet: A deep learning approach for protein-ligand interaction prediction

N Verma, X Qu, F Trozzi, M Elsaied, N Karki… - International journal of …, 2021 - mdpi.com
Computational prediction of Protein-Ligand Interaction (PLI) is an important step in the
modern drug discovery pipeline as it mitigates the cost, time, and resources required to …

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 …

Struct2Graph: a graph attention network for structure based predictions of protein–protein interactions

M Baranwal, A Magner, J Saldinger, ES Turali-Emre… - BMC …, 2022 - Springer
Background Development of new methods for analysis of protein–protein interactions (PPIs)
at molecular and nanometer scales gives insights into intracellular signaling pathways and …

Ligand binding prediction using protein structure graphs and residual graph attention networks

M Pandey, M Radaeva, H Mslati, O Garland… - Molecules, 2022 - mdpi.com
Computational prediction of ligand–target interactions is a crucial part of modern drug
discovery as it helps to bypass high costs and labor demands of in vitro and in vivo …

Multiphysical graph neural network (MP-GNN) for COVID-19 drug design

XS Li, X Liu, L Lu, XS Hua, Y Chi… - Briefings in …, 2022 - academic.oup.com
Graph neural networks (GNNs) are the most promising deep learning models that can
revolutionize non-Euclidean data analysis. However, their full potential is severely curtailed …

Interactiongraphnet: A novel and efficient deep graph representation learning framework for accurate protein–ligand interaction predictions

D Jiang, CY Hsieh, Z Wu, Y Kang, J Wang… - Journal of medicinal …, 2021 - ACS Publications
Accurate quantification of protein–ligand interactions remains a key challenge to structure-
based drug design. However, traditional machine learning (ML)-based methods based on …

Tankbind: Trigonometry-aware neural networks for drug-protein binding structure prediction

W Lu, Q Wu, J Zhang, J Rao, C Li… - Advances in neural …, 2022 - proceedings.neurips.cc
Illuminating interactions between proteins and small drug molecules is a long-standing
challenge in the field of drug discovery. Despite the importance of understanding these …

Multi-PLI: interpretable multi‐task deep learning model for unifying protein–ligand interaction datasets

F Hu, J Jiang, D Wang, M Zhu, P Yin - Journal of cheminformatics, 2021 - Springer
The assessment of protein–ligand interactions is critical at early stage of drug discovery.
Computational approaches for efficiently predicting such interactions facilitate drug …

[HTML][HTML] MM-StackEns: A new deep multimodal stacked generalization approach for protein–protein interaction prediction

AI Albu, MI Bocicor, G Czibula - Computers in Biology and Medicine, 2023 - Elsevier
Accurate in-silico identification of protein–protein interactions (PPIs) is a long-standing
problem in biology, with important implications in protein function prediction and drug …