Journal of the American Society for Mass Spectrometry
Jun 4, 2025
Hydroxyl radical protein footprinting (HRPF) coupled with mass spectrometry yields information about residue solvent exposure and protein topology. However, data from these experiments are sparse and require computational interpretation to generate u...
Recent AI applications have revolutionized the modeling of structurally unresolved protein regions, thereby complementing traditional computational methods. These state-of-the-art techniques can generate numerous candidate structures, significantly e...
Accurate prediction of protein-peptide complex structures plays a critical role in structure-based drug design, including antibody design. Most peptide-docking benchmark studies were conducted using crystal structures of protein-peptide complexes; as...
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...
Journal of chemical information and modeling
May 26, 2025
Interactions between intrinsically disordered proteins (IDPs) are crucial for biological processes, such as intracellular liquid-liquid phase separation (LLPS). Experiments (e.g., NMR) and simulations used to study IDP interactions encounter a variet...
Journal of chemical information and modeling
May 26, 2025
Machine learning algorithms have played a fundamental role in the development of therapeutic antibodies by being trained on data sets of sequences and/or structures. However, structural data sets remain limited, especially those that include antibody...
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...
Journal of chemical information and modeling
May 26, 2025
An effective approach in the development of novel antivirals is to target the assembly of viral capsids by using capsid assembly modulators (CAMs). CAMs targeting hepatitis B virus (HBV) have two major modes of function: they can either accelerate nu...
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...
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...
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