Journal of computer-aided molecular design
Dec 3, 2025
The identification of protein target classes is a key step in drug discovery, as it enables prioritization of screening campaigns and supports target-based drug repurpose. In this study, we developed a deep-learning pipeline based on a multilayer per...
BACKGROUND: Protein function research helps in understanding the complex biological processes that occur within cells. However, the intricate nature of protein structures and functions, along with the rapid growth of protein sequence data, presents a...
Journal of chemical information and modeling
Nov 26, 2025
Protein structure database search has become increasingly challenging due to the growing number of experimental and computational structures. We introduce mTM-align2, a novel two-step approach for rapid and accurate protein structure database search....
ConspectusCovalent chemical labeling of proteins is central to chemical biology, offering functional modifications beyond imaging probes. While genetically engineered systems using self-labeling tags (e.g., HaloTag, SNAP-Tag) or genetic code expansio...
BACKGROUND: Accurate prediction of drug-target interactions (DTIs) is essential for advancing drug discovery. Although numerous computational methods have been proposed, many exhibit limited generalization, particularly when dealing with unseen drugs...
ATP, a high-energy phosphate compound also known as adenosine triphosphate, serves as a direct energy source for living organisms. Proteins, composed of amino acids, are fundamental macromolecules and essential building blocks of life. The interactio...
Journal of computer-aided molecular design
Nov 25, 2025
Antimicrobial Resistance (AMR) is a global concern demanding high-throughput and precise AMR surveillance strategies. This review provides a comprehensive list of Artificial Intelligence (AI) driven frameworks widely employed in the early detection, ...
Journal of chemical information and modeling
Nov 20, 2025
Accurate prediction of compound-protein interactions (CPIs) is critical for drug discovery, but existing data sets often suffer from biases that hinder model generalization. Here, we first highlighted that over-represented molecular scaffolds and imb...
In living organisms, proteins perform key functions required for life activities by interacting to form complexes. Determining the protein complex structure is crucial for understanding and mastering biological functions. Although AlphaFold2 makes a ...
Physical chemistry chemical physics : PCCP
Nov 19, 2025
Protein-ligand binding affinity prediction plays a crucial role in drug discovery. While recent works use two-dimensional graph neural networks to improve affinity prediction, we find that the three-dimensional geometric information of proteins and l...
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