The most popular and universally predictive protein simulation models employ all-atom molecular dynamics, but they come at extreme computational cost. The development of a universal, computationally efficient coarse-grained (CG) model with similar pr...
Accurate dynamic protein structures are essential for drug design. NMR experiments can detect protein structures and potential dynamics, but the spectrum assignment and structure determination requires expertise and is time-consuming, while deep-lear...
Progress in biophysics and molecular biology
Jul 17, 2025
Currently, computational protein design (CPD) is a disruptive force in biotechnology, changing the paradigm by which proteins are engineered for many applications. In this article, the evolution of CPD has been tracked from its initial forays in the ...
Journal of chemical information and modeling
Jul 16, 2025
Scoring biomolecular complexes remains central to structural modeling efforts. Recent studies suggest that AlphaFold (AF) - a revolutionary deep learning model for biomolecular structure prediction - has implicitly learned an approximate biophysical ...
Journal of chemical theory and computation
Jul 14, 2025
In this study, we propose a Kernel-PCA model designed to capture structure-function relationships in a protein. This model also enables the ranking of reaction coordinates according to their impact on protein properties. By leveraging machine learnin...
Journal of computer-aided molecular design
Jul 13, 2025
Identifying orthosteric binding sites and predicting small molecule affinities remains a key challenge in virtual screening. While blind docking explores the entire protein surface, its precision is hindered by the vast search space. Cavity detection...
BACKGROUND: Predicting protein structural similarity and detecting homologous sequences remain fundamental and challenging tasks in computational biology. Accurate identification of structural homologs enables function inference for newly discovered ...
Journal of chemical information and modeling
Jul 8, 2025
Peptide toxicity prediction is a critical task in biomedical research, influencing drug safety and therapeutic development. Traditional methods, relying on sequence similarity or handcrafted features, struggle to capture the complex relationship betw...
BACKGROUND: Proteins self-organize in dynamic cellular environments by assembling into reversible biomolecular condensates through liquid-liquid phase separation (LLPS). These condensates can comprise single or multiple proteins, with different roles...
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