The process of virtual screening relies heavily on the databases, but it is disadvantageous to conduct virtual screening based on commercial databases with patent-protected compounds, high compound toxicity and side effects. Therefore, this paper uti...
Journal of chemical information and modeling
38648077
Machine learning has the potential to provide tremendous value to life sciences by providing models that aid in the discovery of new molecules and reduce the time for new products to come to market. Chemical reactions play a significant role in these...
Journal of chemical information and modeling
38950894
Information extraction from chemistry literature is vital for constructing up-to-date reaction databases for data-driven chemistry. Complete extraction requires combining information across text, tables, and figures, whereas prior work has mainly inv...
Journal of chemical information and modeling
39302256
A knowledge graph (KG) is a technique for modeling entities and their interrelations. Knowledge graph embedding (KGE) translates these entities and relationships into a continuous vector space to facilitate dense and efficient representations. In the...
Journal of chemical information and modeling
39602490
Cyanobacteria strains have the potential to produce bioactive compounds that can be used in therapeutics and bioremediation. Therefore, compiling all information about these compounds to consider their value as bioresources for industrial and researc...
Journal of molecular graphics & modelling
39561662
Acetylcholinesterase (AChE) is one of the most successful targets for the treatment of Alzheimer's disease (AD). Inhibition of AChE can result in preventing AD. In this context, the machine-learning (ML) model, molecular docking, and molecular dynami...
The NLRP3 inflammasome, plays a critical role in the pathogenesis of rheumatoid arthritis (RA) by activating inflammatory cytokines such as IL1β and IL18. Targeting NLRP3 has emerged as a promising therapeutic strategy for RA. In this study, a multid...
Journal of chemical information and modeling
39656869
While data curation principles and practices are a major topic in data science, they are often not explicitly considered in machine learning (ML) applications in chemistry. We have been interested in evaluating the potential effects of data curation ...
OBJECTIVES: Beta-lactamase is a bacterial enzyme that deactivates beta-lactam antibiotics, and it is one of the leading causes of antibiotic resistance problems globally. In current drug discovery research, molecular simulation, like molecular dockin...
When applying machine learning (ML) approaches for the prediction of bioactivity, it is common to collect data from different assays or sources and combine them into single data sets. However, depending on the data domains and sources from which thes...