INTRODUCTION: Artificial intelligence (AI) has emerged as a transformative tool in drug discovery, particularly in virtual screening (VS), a crucial initial step in identifying potential drug candidates. This article highlights the significance of AI...
Glycosaminoglycans (GAGs) are linear, negatively charged carbohydrates that modulate enzymatic activity in the extracellular matrix. Their high flexibility and specificity in protein-GAG interactions pose challenges for both experimental and computat...
Journal of chemical information and modeling
Jun 9, 2025
Dysfunctions of the dopamine D2 and D3 receptors (D2 and D3) are implicated in neuropsychiatric conditions such as Parkinson's disease, schizophrenia, and substance use disorders (SUDs). Evidence indicates that D3-selective ligands can effectively mo...
Journal of chemical information and modeling
Jun 9, 2025
The leucine-rich repeat kinase 2 (LRRK2) is the most mutated gene in familial Parkinson's disease, and its mutations lead to pathogenic hallmarks of the disease. The LRRK2 WDR domain is an understudied drug target for Parkinson's disease, with no kno...
The pharmaceutical industry faces persistent challenges in developing effective treatments for complex diseases, creating an urgent need for innovative approaches to accelerate drug discovery. A pivotal factor in this process is the accurate predicti...
Journal of chemical information and modeling
May 26, 2025
The fusion of traditional chemical descriptors with graph neural networks (GNNs) offers a compelling strategy for enhancing ligand-based virtual screening methodologies. A comprehensive evaluation revealed that the benefits derived from this integrat...
Deep learning has advanced the design of static protein structures, but the controlled conformational changes that are hallmarks of natural signaling proteins have remained inaccessible to de novo design. Here, we describe a general deep learning-gui...
International journal of molecular sciences
May 14, 2025
Cryptic sites, which are transient binding sites that emerge through protein conformational changes upon ligand binding, are valuable targets for drug discovery, particularly for allosteric modulators. However, identifying these sites remains challen...
International journal of molecular sciences
May 14, 2025
Engineered scaffold-based proteins that bind to concrete targets with high affinity offer significant advantages over traditional antibodies in theranostic applications. Their development often relies on display methods, where large libraries of vari...
Journal of chemical theory and computation
May 13, 2025
The dissociation or off rate, , of a drug molecule has been shown to be more relevant to efficacy than affinity for selected systems, motivating the development of predictive computational methodologies. These are largely based on enhanced-sampling m...
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