Related papers: SCOPE-DTI: Semi-Inductive Dataset Construction and…

Drug-drug interaction (DDI) prediction is a critical task in computational biomedicine, as adverse interactions between co-administered drugs can cause severe side effects and clinical risks. A key challenge is unseen-drug generalization,…

The identification of compound-protein interactions (CPI) plays a critical role in drug screening, drug repurposing, and combination therapy studies. The effectiveness of CPI prediction relies heavily on the features extracted from both…

Significant differences in protein structures hinder the generalization of existing drug-target interaction (DTI) models, which often rely heavily on pre-learned binding principles or detailed annotations. In contrast, BioBridge designs an…

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…

Accurate prediction of compound-protein interactions (CPI) remains a cornerstone challenge in computational drug discovery. While existing sequence-based approaches leverage molecular fingerprints or graph representations, they critically…

The Interaction between Drugs and Targets (DTI) in human body plays a crucial role in biomedical science and applications. As millions of papers come out every year in the biomedical domain, automatically discovering DTI knowledge from…

Background: Discovering potential drug-drug interactions (DDIs) is a long-standing challenge in clinical treatments and drug developments. Recently, deep learning techniques have been developed for DDI prediction. However, they generally…

Drug-drug interactions (DDIs) can result in various pharmacological changes, which can be categorized into different classes known as DDI events (DDIEs). In recent years, previously unobserved/unseen DDIEs have been emerging, posing a new…

Many machine learning models, such as logistic regression~(LR) and support vector machine~(SVM), can be formulated as composite optimization problems. Recently, many distributed stochastic optimization~(DSO) methods have been proposed to…

Drug-drug interactions (DDIs) are a major concern in polypharmacy. Public databases often provide only qualitative descriptions without pharmacokinetic context. We present an interactive web tool that integrates 191,541 descriptive DDI…

Accurate prediction of drug response in precision medicine requires models that capture how specific chemical substructures interact with cellular pathway states. However, most existing deep learning approaches treat chemical and…

Drug-target interaction (DTI) prediction is crucial for drug development and repositioning. Methods using heterogeneous graph neural networks (HGNNs) for DTI prediction have become a promising approach, with attention-based models often…

Predicting drug-drug interactions (DDI) is the problem of predicting side effects (unwanted outcomes) of a pair of drugs using drug information and known side effects of many pairs. This problem can be formulated as predicting labels (i.e.…

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…

Drug-drug interaction (DDI) is a vital information when physicians and pharmacists intend to co-administer two or more drugs. Thus, several DDI databases are constructed to avoid mistakenly combined use. In recent years, automatically…

Drug membrane interaction is a very significant bioprocess to consider in drug discovery. Here, we propose a novel deep learning framework coined DMInet to study drug-membrane interactions that leverages large-scale Martini coarse-grained…

Drug-target relationships may now be predicted computationally using bioinformatics data, which is a valuable tool for understanding pharmacological effects, enhancing drug development efficiency, and advancing related research. A number of…

Drug combinations are essential in cancer therapy, leveraging synergistic drug-drug interactions (DDI) to enhance efficacy and combat resistance. However, the vast combinatorial space makes experimental screening impractical, and existing…

Minimizing adverse reactions caused by drug-drug interactions has always been a momentous research topic in clinical pharmacology. Detecting all possible interactions through clinical studies before a drug is released to the market is a…

Drug-drug interactions (DDIs) are a major concern in clinical practice, as they can lead to reduced therapeutic efficacy or severe adverse effects. Traditional computational approaches often struggle to capture the complex relationships…