Artificial intelligence is revolutionizing structural bioinformatics, with AlphaFold arguably being the most impactful development to date. The structural atlases generated by these methods present significant opportunities for unraveling biological ...
Yu Xue is a professor in the College of Life Science and Technology at Huazhong University of Science and Technology, and hold a joint position in the Hubei Hongshan Laboratory at Huazhong Agricultural University. He received two B.E. degrees in poly...
Journal of chemical information and modeling
Oct 9, 2025
Drug-Target Interaction (DTI) prediction is an indispensable process in drug repositioning. Wet-lab experiments for potential DTI identification are reliable but expensive, labor-intensive, and time-consuming. Deep learning demonstrates the superior ...
Having an accurate reaction coordinate (RC) is essential for reliable kinetic characterization of molecular processes, but there are few quantitative metrics to evaluate RC quality. In this study, we consider the dimensionless γ metric from the Expon...
Journal of computer-aided molecular design
Oct 7, 2025
Drug discovery relies on the ability to predict drug-target affinity (DTA), which allows for the efficient identification of drug candidates for certain protein targets. Scalability, accuracy, and interpretability are issues that traditional methods ...
Proceedings of the National Academy of Sciences of the United States of America
Oct 6, 2025
Deep generative models have demonstrated success in learning the protein sequence to function relationship and designing synthetic sequences with engineered functionality. We introduce the Protein Transformer Variational AutoEncoder (ProT-VAE) as an ...
Co-folding models represent a major innovation in deep-learning-based protein-ligand structure prediction. The recent publications of RoseTTAFold All-Atom, AlphaFold3, and others have shown high-quality results on predicting the structures of protein...
Journal of computer-aided molecular design
Oct 6, 2025
Protein pockets, or small cavities on the protein surface, are critical sites for enzymatic catalysis, molecular recognition, and drug binding. Accurately identifying these pockets is crucial for understanding protein function and designing therapeut...
Journal of chemical information and modeling
Oct 3, 2025
Accurately predicting protein-ligand binding affinity (PLA) is essential in drug discovery for identifying lead compounds. The sequence and structural contexts of an amino acid residue (i.e., microenvironment) describe the surrounding chemical proper...
Journal of chemical information and modeling
Oct 3, 2025
Network methods and molecular dynamics (MD) simulations have become essential tools for studying protein dynamics. However, applying network methods to MD simulations of flexible proteins is a major challenge, since the high conformational heterogene...
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