AIMC Topic: Amino Acid Sequence
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CPPCGM: A Highly Efficient Sequence-Based Tool for Simultaneously Identifying and Generating Cell-Penetrating Peptides.
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...
Artificial intelligence-powered prediction of AIM-2 inflammasome sequences using transformers and graph attention networks in periodontal inflammation.
Scientific reports
Mar 13, 2025
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...
Machine learning methods to study sequence-ensemble-function relationships in disordered proteins.
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...
Development of DeepPQK and DeepQK sequence-based deep learning models to predict protein-ligand affinity and application in the directed evolution of ferulic esterase DLfae4.
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...
Identification and taste presentation characteristics of umami peptides from soybean paste based on peptidomics and virtual screening.
Food chemistry
Feb 25, 2025
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...
Enhancing Functional Protein Design Using Heuristic Optimization and Deep Learning for Anti-Inflammatory and Gene Therapy Applications.
Proteins
Feb 22, 2025
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...
Cloning, Characterization, and Computer-Aided Evolution of a Thermostable Laccase of the DUF152 Family From Klebsiella michiganensis.
Proteins
Feb 14, 2025
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...
Simpler Protein Domain Identification Using Spectral Clustering.
Proteins
Feb 13, 2025
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...
Intelligent decoding platform for peptide sequences: SERS detection via high affinity self-assembled silver nanoparticles and machine learning analysis.
Analytica chimica acta
Feb 13, 2025
BACKGROUND: Peptides are compounds formed by the dehydration-condensation reaction of two or more amino acids which play an important role in the life functions of the organism. Changes in the structure of amino acids and peptides are vital for eluci...
Deep Learning-Assisted Discovery of Protein Entangling Motifs.
Biomacromolecules
Feb 12, 2025
Natural topological proteins exhibit unique properties including enhanced stability, controlled quaternary structures, and dynamic switching properties, highlighting topology as a unique dimension in protein engineering. Although artificial design an...
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