Chemical reviews
May 28, 2025
Biomolecules present promising stimuli-responsive mechanisms to revolutionize soft actuators. Proteins, peptides, and nucleic acids foster specific intermolecular interactions, and their boundless sequence design spaces encode precise actuation capab...
Journal of chemical theory and computation
May 27, 2025
Proteins are inherently dynamic molecules, and their conformational transitions among various states are essential for numerous biological processes, which are often modulated by their interactions with surrounding environments. Although molecular dy...
Biomaterials science
May 27, 2025
Interrogation of the secondary structures of proteins is essential for designing and engineering more effective and safer protein-based biomaterials and other classes of theranostic materials. Protein secondary structures are commonly assessed using ...
Journal of chemical information and modeling
May 26, 2025
Physics-based docking methods have long been the cornerstone of structure-based virtual screening (VS). However, the emergence of machine learning (ML)-based docking approaches has opened new possibilities for enhancing VS technologies. In this study...
Science (New York, N.Y.)
May 22, 2025
Deep learning has advanced the design of static protein structures, but the controlled conformational changes that are hallmarks of natural signaling proteins have remained inaccessible to de novo design. Here, we describe a general deep learning-gui...
The journal of physical chemistry. B
May 22, 2025
Computational techniques such as all-atom (AA) molecular dynamics (MD) simulations and coarse-grained (CG) models have been essential to study various biological problems over a wide range of scales. While AA simulations provide detailed insights, th...
International journal of molecular sciences
May 14, 2025
Cryptic sites, which are transient binding sites that emerge through protein conformational changes upon ligand binding, are valuable targets for drug discovery, particularly for allosteric modulators. However, identifying these sites remains challen...
Scientific reports
May 14, 2025
The stability of proteins at higher temperatures is crucial for their functionality, which is measured by their melting temperature (Tm). The Tm is the temperature at which 50% of the protein loses its native structure and activity. Existing methods ...
Journal of chemical theory and computation
May 13, 2025
The dissociation or off rate, , of a drug molecule has been shown to be more relevant to efficacy than affinity for selected systems, motivating the development of predictive computational methodologies. These are largely based on enhanced-sampling m...
Journal of chemical theory and computation
May 13, 2025
Machine learning has emerged as a promising approach for predicting molecular properties of proteins, as it addresses limitations of experimental and traditional computational methods. Here, we introduce GSnet, a graph neural network (GNN) trained to...