Allosteric molecules provide a powerful means to modulate protein function. However, the effect of such ligands on distal orthosteric sites cannot be easily described by classical docking methods. Here, we applied machine learning (ML) approaches to ...
Binding sites in proteins can be either specifically functional binding sites (active sites) that bind specific substrates with high affinity or regulatory binding sites (allosteric sites), that modulate the activity of functional binding sites throu...
Designing highly selective compounds to protein subtypes and developing allosteric modulators targeting them are critical considerations to both drug discovery and mechanism studies for cannabinoid receptors. It is challenging but in demand to have c...
Predicting drug-protein interactions (DPIs) for target proteins involved in dopamine pathways is a very important goal in medicinal chemistry. We can tackle this problem using Molecular Docking or Machine Learning (ML) models for one specific protein...
Journal of biomolecular structure & dynamics
Mar 2, 2018
Thrombin is a key component for chemotherapeutic and antithrombotic therapy development. As the physiologic and pathologic roles of the light chain still remain vague, here, we continue previous efforts to understand the impacts of the disease-associ...
Protein-protein interactions (PPIs) are ubiquitous mediators of cellular functions, and their dysregulation is central to numerous pathological conditions. Traditional drug discovery strategies targeting PPIs directly have faced considerable obstacle...
Allosteric regulation of protein function, where a perturbation at one site induces a conformational shift or alters dynamics at a distal functional site, plays a key role in numerous biological processes. The ability to introduce allostery using syn...
Journal of chemical information and modeling
Jul 14, 2025
TAK1, a multifunctional kinase, possesses intramolecular interactions that are capacitated to recognize and process diverse forms of chemical and mechanical forces, which ultimately translate into a convergent catalytic function. By elucidating a dua...
Journal of agricultural and food chemistry
Jul 9, 2025
Most CYP51 inhibitors act competitively and are prone to resistance, whereas allosteric inhibitors hold promise but are difficult to develop. In this study, we employed the neural relational inference framework alongside the Gaussian network-based de...
Undruggable targets are those of therapeutical significance but challenging for conventional drug design approaches. Such targets often exhibit unique features, including highly dynamic structures, a lack of well-defined ligand-binding pockets, the p...
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