We have evaluated the prediction accuracy of three different tools, deep-learning-based AlphaFold2, AlphaFold3, and large language model-based ESMFold, utilizing the experimentally derived structures deposited in the Protein Data Bank between 2022 an...
Physical chemistry chemical physics : PCCP
Jan 14, 2026
Recent advances in machine learning and self-supervised deep language modeling have made it possible to accurately predict protein structural properties. Most existing models and pretraining methods leverage evolutionary information in multiple seque...
Recent breakthroughs in protein structure prediction have opened new avenues for genome-wide drug discovery, yet existing virtual screening methods remain computationally prohibitive. We present DrugCLIP, a contrastive learning framework that achieve...
Journal of chemical information and modeling
Dec 30, 2025
The ability of proteins to adopt multiple conformations is fundamental to their biological function. With the advent of AlphaFold, machine learning (ML)-based methods have extended their capabilities to more broadly sample this intrinsic conformation...
Proceedings of the National Academy of Sciences of the United States of America
Dec 24, 2025
Understanding protein structure and dynamics is crucial for basic biology and drug design. Conventional methods often provide static conformations that inadequately capture protein flexibility. We present PackDock, a framework that integrates deep le...
Journal of chemical information and modeling
Dec 22, 2025
The accurate prediction of protein-ligand binding poses and affinities is central to structure-based drug design. In this study, we first benchmarked three distinct pose generation strategies for data sets from the ASAP Antiviral Challenge 2025: mole...
Journal of the American Society for Mass Spectrometry
Dec 21, 2025
Recent advances in ion mobility spectrometry have enabled the measurement of rotationally averaged collisional cross-sectional area (CCS) for millions of peptides as part of routine proteomic mass spectrometry workflows. One of the most striking find...
Voltage-gated sodium (NaV) channels are vital regulators of electrical activity in excitable cells. Given their importance in physiology, NaV channels are key therapeutic targets for treating numerous conditions, yet developing subtype-selective drug...
The rapid evolution of molecular dynamics (MD) methods, including machine-learned dynamics, has outpaced the development of standardized tools for method validation. Objective comparison between simulation approaches is often hindered by inconsistent...
Chemical and conformational changes are crucial to protein function and its pharmacological control. X-ray crystallography can reveal these changes in atomic detail, but standard analysis methods, which refine separate datasets, often overlook differ...
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