Preserving proteome integrity is crucial for maintaining cell viability across all kingdoms of life. The bacterial caseinolytic protease (ClpP) plays a critical role in maintaining protein homeostasis by degrading misfolded or damaged proteins within...
Cryo-EM and X-ray crystallography provide crucial experimental data for obtaining atomic-detail models of biomacromolecules. Refining these models relies on library-based stereochemical data, which, in addition to being limited to known chemical enti...
Journal of chemical information and modeling
Oct 14, 2025
Pose prediction of ligands to proteins remains a central challenge of structure-based drug design. Although data leakage and generalizability concerns remain, data-driven methods for pose prediction (i.e., based on deep learning and diffusion) now ro...
Journal of chemical information and modeling
Oct 13, 2025
β-Arrestins (βarr1 and βarr2) are key transducers of G protein-coupled receptor (GPCR) signaling, orchestrating both shared and isoform-specific intracellular pathways. Phosphorylation of the receptor C-terminal tail by GPCR kinases encodes regulator...
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 ...
Proceedings of the National Academy of Sciences of the United States of America
Oct 10, 2025
While deep learning has advanced protein sequence and function design, engineering highly active and stable proteins still requires labor-intensive iterative computational design and experimentation. There is a critical need for methods capable of di...
Intrinsically disordered proteins and regions (IDRs) lack stable 3D structures, posing challenges for interaction prediction. We present SpatPPI, a geometric deep learning model tailored for IDPPI prediction. SpatPPI leverages structural cues from fo...
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
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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