Computer methods and programs in biomedicine
Mar 30, 2025
BACKGROUND AND OBJECTIVE: Protein-protein interactions (PPIs) play the key roles in myriad biological processes, helping to understand the protein function and disease pathology. Identification of PPIs and their interaction types through wet experime...
Protein sequence design in the context of small molecules, nucleotides and metals is critical to enzyme and small-molecule binder and sensor design, but current state-of-the-art deep-learning-based sequence design methods are unable to model nonprote...
Journal of chemical information and modeling
Mar 19, 2025
Cell-penetrating peptides (CPPs) are usually short oligopeptides with 5-30 amino acid residues. CPPs have been proven as important drug delivery vehicles into cells through different mechanisms, demonstrating their potential as therapeutic candidates...
Periodontal inflammation is a chronic condition affecting the tissues surrounding teeth. Initiated by dental plaque, it triggers an immune response leading to tissue destruction. The AIM-2 inflammasome regulates this response, and understanding its p...
Current opinion in structural biology
Mar 12, 2025
Recent years have seen tremendous developments in the use of machine learning models to link amino-acid sequence, structure, and function of folded proteins. These methods are, however, rarely applicable to the wide range of proteins and sequences th...
International journal of biological macromolecules
Mar 5, 2025
Affinity plays an essential role in the rate and stability of enzyme-catalyzed reactions, thus directly impacting the catalytic activity. In general, the predictive method for protein-ligand binding affinity mainly relies on high-resolution protein c...
This research concentrated on soybean paste fermented with Tetragenococcus halophilus, employing peptidomics and machine learning methodologies to screen for novel umami peptides. Taste characteristics of umami peptides were evaluated through sensory...
Protein sequence design is a highly challenging task, aimed at discovering new proteins that are more functional and producible under laboratory conditions than their natural counterparts. Deep learning-based approaches developed to address this prob...
Bacterial laccases exhibit relatively high optimal reaction temperatures and possess a broad substrate spectrum, thereby expanding the range of potential applications for laccase enzymes. This study aims to investigate the molecular evolution of bact...
The decomposition of a biomolecular complex into domains is an important step to investigate biological functions and ease structure determination. A successful approach to do so is the SPECTRUS algorithm, which provides a segmentation based on spect...
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