Related papers: Decoding the Protein-ligand Interactions Using Par…

Prediction of protein-ligand interactions (PLI) plays a crucial role in drug discovery as it guides the identification and optimization of molecules that effectively bind to target proteins. Despite remarkable advances in deep…

Neural Networks (GNNs) have revolutionized the molecular discovery to understand patterns and identify unknown features that can aid in predicting biophysical properties and protein-ligand interactions. However, current models typically…

The study of multi-type Protein-Protein Interaction (PPI) is fundamental for understanding biological processes from a systematic perspective and revealing disease mechanisms. Existing methods suffer from significant performance degradation…

Protein-protein interactions (PPIs) play key roles in a broad range of biological processes. Numerous strategies have been proposed for predicting PPIs, and among them, graph-based methods have demonstrated promising outcomes owing to the…

Expanding the scope of graph-based, deep-learning models to noncovalent protein-ligand interactions has earned increasing attention in structure-based drug design. Modeling the protein-ligand interactions with graph neural networks (GNNs)…

We introduce Bi-GNN for modeling biological link prediction tasks such as drug-drug interaction (DDI) and protein-protein interaction (PPI). Taking drug-drug interaction as an example, existing methods using machine learning either only…

The prediction of protein-ligand binding affinity is of great significance for discovering lead compounds in drug research. Facing this challenging task, most existing prediction methods rely on the topological and/or spatial structure of…

Drug discovery often relies on the successful prediction of protein-ligand binding affinity. Recent advances have shown great promise in applying graph neural networks (GNNs) for better affinity prediction by learning the representations of…

Protein-protein interactions (PPIs) are crucial in various biological processes and their study has significant implications for drug development and disease diagnosis. Existing deep learning methods suffer from significant performance…

Binding affinity prediction of three-dimensional (3D) protein ligand complexes is critical for drug repositioning and virtual drug screening. Existing approaches transform a 3D protein-ligand complex to a two-dimensional (2D) graph, and…

Recent advances in Natural Language Processing (NLP) have ignited interest in developing effective methods for predicting protein-ligand interactions (PLIs) given their relevance to drug discovery and protein engineering efforts and the…

The protein-ligand binding affinity (PLA) prediction goal is to predict whether or not the ligand could bind to a protein sequence. Recently, in PLA prediction, deep learning has received much attention. Two steps are involved in deep…

Accurate prediction of drug-target interaction (DTI) is essential for in silico drug design. For the purpose, we propose a novel approach for predicting DTI using a GNN that directly incorporates the 3D structure of a protein-ligand…

Motivation: Drug discovery demands rapid quantification of compound-protein interaction (CPI). However, there is a lack of methods that can predict compound-protein affinity from sequences alone with high applicability, accuracy, and…

Protein dynamics play a crucial role in many biological processes and drug interactions. However, measuring, and simulating protein dynamics is challenging and time-consuming. While machine learning holds promise in deciphering the…

Efficient and effective drug-target binding affinity (DTBA) prediction is a challenging task due to the limited computational resources in practical applications and is a crucial basis for drug screening. Inspired by the good representation…

Explainable Graph Neural Networks (GNNs) have been developed and applied to drug-protein binding prediction to identify the key chemical structures in a drug that have active interactions with the target proteins. However, the key…

Protein-protein interactions (PPIs) play a crucial role in numerous biological processes. Developing methods that predict binding affinity changes under substitution mutations is fundamental for modelling and re-engineering biological…

Multi-scale biomedical knowledge networks are expanding with emerging experimental technologies that generates multi-scale biomedical big data. Link prediction is increasingly used especially in bipartite biomedical networks to identify…

Explainable artificial intelligence (XAI) approaches have been increasingly applied in drug discovery to learn molecular representations and identify substructures driving property predictions. However, building end-to-end explainable…