ConspectusEnhanced-sampling techniques employed in free-energy calculations overcome the limitations of brute-force molecular dynamics (MD) and are widely used to interrogate complex biological and chemical systems at atomic resolution. Depending on ...
Journal of chemical information and modeling
Dec 17, 2025
The accurate identification of drug-target interactions is crucial for shortening the timeline and lowering the expenses of pharmaceutical research, as the discovery of novel drugs remains a highly complex, resource-intensive, and lengthy endeavor. D...
Journal of chemical information and modeling
Dec 15, 2025
Quantitative prediction of binding affinity in protein-protein interactions is critical for deciphering biological mechanisms and advancing therapeutic antibody development. While experimental methods for measuring binding affinity remain limited by ...
Air pollution poses a critical global public health challenge. Molecular-level initiating events, such as pollutant-protein interactions, can trigger cascades of biological responses that may contribute to adverse health effects. However, current met...
Journal of chemical information and modeling
Dec 9, 2025
Accurate prediction of drug-target interactions (DTIs) is essential for drug discovery and repurposing. Despite recent advances, deep learning models often exhibit limited generalization under realistic cold-start scenarios and suffer from poor inter...
Journal of chemical information and modeling
Dec 8, 2025
With the continued exploration of biological resources in extreme environments, functional proteins such as acidophilic proteins have attracted increasing attention. These proteins can maintain structural stability and biological functionality under ...
The rapid evolution of molecular dynamics (MD) methods, including machine-learned dynamics, has outpaced the development of standardized tools for method validation. Objective comparison between simulation approaches is often hindered by inconsistent...
Deep learning (DL) algorithms have increasingly been applied to predict protein-ligand binding affinity, a critical step in drug design. Yet, many models still struggle to generalize to unseen data, and when coupled with the absence of confidence est...
Journal of chemical information and modeling
Dec 3, 2025
Developing effective computational representations of protein sequences is crucial for advancing diverse areas of computational biology and bioinformatics. Ideal representations must be computationally efficient, scalable, informative, flexible acros...
Chemical and conformational changes are crucial to protein function and its pharmacological control. X-ray crystallography can reveal these changes in atomic detail, but standard analysis methods, which refine separate datasets, often overlook differ...
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