Journal of chemical information and modeling
Sep 1, 2025
Sigma (σ) receptors (SRs) have emerged as important therapeutic targets due to their roles in various biological pathways. They are classified into two subtypes: S1R, primarily distributed in the central nervous system and related to neuroprotection ...
Journal of the American Chemical Society
Aug 21, 2025
Detecting protein biomarkers is critical in fundamental research and clinical investigations of extracellular vesicles (EVs). Despite the prevalent use of antibodies as recognition elements, their application is often limited by challenges such as cr...
Journal of chemical information and modeling
Aug 18, 2025
Achieving structural novelty in drug discovery remains a critical challenge. Artificial intelligence (AI) has demonstrated remarkable potential in deciphering the complex relationships between molecular structures and activities from vast amounts of ...
Journal of chemical information and modeling
Aug 14, 2025
Identifying functional sites of RNA, particularly those where small molecules bind, is crucial for understanding related biological processes and advancing drug design. Small molecule therapies, compared to traditional protein-targeted therapies, hav...
Auranofin, an FDA-approved antirheumatic gold drug, has gained ongoing interest in clinical studies for treating advanced or recurrent tumors. However, gold ion's dynamic thiol exchange nature strongly attenuates its bioactivity due to the fast forma...
Journal of chemical theory and computation
Aug 5, 2025
Binding free energies are key elements in understanding and predicting the strength of protein-drug interactions. While classical free energy simulations yield good results for many purely organic ligands, drugs, including transition metal atoms, oft...
Protein-ligand interactions play central roles in myriad biological processes and are of key importance in drug design. Deep learning approaches are becoming cost-effective alternatives to high-throughput experimental methods for ligand identificatio...
Journal of chemical information and modeling
Jul 25, 2025
Machine learning has become an essential tool in computational drug design, enabling models to uncover patterns in molecular data and predict protein-ligand interactions. This study introduces a novel approach by integrating persistence images with M...
Journal of chemical information and modeling
Jul 25, 2025
To understand the benefits and drawbacks of 3D combinatorial and deep learning generators, a novel benchmark was created focusing on the recreation of important protein-ligand interactions and 3D ligand conformations. Using the BindingMOAD data set w...
Journal of chemical information and modeling
Jul 16, 2025
Scoring biomolecular complexes remains central to structural modeling efforts. Recent studies suggest that AlphaFold (AF) - a revolutionary deep learning model for biomolecular structure prediction - has implicitly learned an approximate biophysical ...
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