Related papers: DeepPurpose: a Deep Learning Library for Drug-Targ…

Motivation: Predicting the drug-target interaction is crucial for drug discovery as well as drug repurposing. Machine learning is commonly used in drug-target affinity (DTA) problem. However, machine learning model faces the cold-start…

Traditional drug discovery processes are both time-consuming and require extensive professional expertise. With the accumulation of drug-target interaction (DTI) data from experimental studies, leveraging modern machine-learning techniques…

Predicting compound-protein affinity is critical for accelerating drug discovery. Recent progress made by machine learning focuses on accuracy but leaves much to be desired for interpretability. Through molecular contacts underlying…

Recently, deep neural network (DNN)-based drug-target interaction (DTI) models were highlighted for their high accuracy with affordable computational costs. Yet, the models' insufficient generalization remains a challenging problem in the…

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: Exploring drug-protein interactions (DPIs) work as a pivotal step in drug discovery. The fast expansion of available biological data enables computational methods effectively assist in experimental methods. Among them, deep…

Background: Drug-drug interactions (DDIs) refer to processes triggered by the administration of two or more drugs leading to side effects beyond those observed when drugs are administered by themselves. Due to the massive number of possible…

Detecting probable Drug Target Interaction (DTI) is a critical task in drug discovery. Conventional DTI studies are expensive, labor-intensive, and take a lot of time, hence there are significant reasons to construct useful computational…

Predicting and discovering drug-drug interactions (DDIs) using machine learning has been studied extensively. However, most of the approaches have focused on text data or textual representation of the drug structures. We present the first…

With the development of computer-assisted techniques, research communities including biochemistry and deep learning have been devoted into the drug discovery field for over a decade. Various applications of deep learning have drawn great…

The increasing volume of drug combinations in modern therapeutic regimens needs reliable methods for predicting drug-drug interactions (DDIs). While Large Language Models (LLMs) have revolutionized various domains, their potential in…

The efficacy of a drug depends on its binding affinity to the therapeutic target and pharmacokinetics. Deep learning (DL) has demonstrated remarkable progress in predicting drug efficacy. We develop MolDesigner, a human-in-the-loop web…

Accurate prediction of drug-target binding affinity can accelerate drug discovery by prioritizing promising compounds before costly wet-lab screening. While deep learning has advanced this task, most models fuse ligand and protein…

Computational models that accurately predict the binding affinity of an input protein-chemical pair can accelerate drug discovery studies. These models are trained on available protein-chemical interaction datasets, which may contain…

Predicting unknown drug-drug interactions (DDIs) is crucial for improving medication safety. Previous efforts in DDI prediction have typically focused on binary classification or predicting DDI categories, with the absence of explanatory…

Accurately predicting drug-target binding affinity (DTA) in silico is a key task in drug discovery. Most of the conventional DTA prediction methods are simulation-based, which rely heavily on domain knowledge or the assumption of having the…

Identification of drug-target interactions is an indispensable part of drug discovery. While conventional shallow machine learning and recent deep learning methods based on chemogenomic properties of drugs and target proteins have pushed…

Adverse drug-drug interactions~(DDIs) can compromise the effectiveness of concurrent drug administration, posing a significant challenge in healthcare. As the development of new drugs continues, the potential for unknown adverse effects…

The first step in drug discovery is finding drug molecule moieties with medicinal activity against specific targets. Therefore, it is crucial to investigate the interaction between drug-target proteins and small chemical molecules. However,…

Artificial intelligence (AI) in the form of deep learning bears promise for drug discovery and chemical biology, $\textit{e.g.}$, to predict protein structure and molecular bioactivity, plan organic synthesis, and design molecules…