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Attention-aware differential learning for predicting peptide-MHC class I binding and T cell receptor recognition.
Brief Bioinform
November 2024
School of Computer Science, Northwestern Polytechnical University, Xi'an, 710129 Shaanxi, China.
The identification of neoantigens is crucial for advancing vaccines, diagnostics, and immunotherapies. Despite this importance, a fundamental question remains: how to model the presentation of neoantigens by major histocompatibility complex class I molecules and the recognition of the peptide-MHC-I (pMHC-I) complex by T cell receptors (TCRs). Accurate prediction of pMHC-I binding and TCR recognition remains a significant computational challenge in immunology due to intricate binding motifs and the long-tail distribution of known binding pairs in public databases.
View Article and Find Full Text PDFA comprehensive benchmarking for evaluating TCR embeddings in modeling TCR-epitope interactions.
Brief Bioinform
November 2024
Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong, 999077, China.
The complexity of T cell receptor (TCR) sequences, particularly within the complementarity-determining region 3 (CDR3), requires efficient embedding methods for applying machine learning to immunology. While various TCR CDR3 embedding strategies have been proposed, the absence of their systematic evaluations created perplexity in the community. Here, we extracted CDR3 embedding models from 19 existing methods and benchmarked these models with four curated datasets by accessing their impact on the performance of TCR downstream tasks, including TCR-epitope binding affinity prediction, epitope-specific TCR identification, TCR clustering, and visualization analysis.
View Article and Find Full Text PDFUnravelling the aromatic symphony: redirecting bifunctional mushroom synthases towards linalool monofunctionality.
Adv Biotechnol (Singap)
January 2025
Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.
Enzymes are the cornerstone of biocatalysis, biosynthesis and synthetic biology. However, their applicability is often limited by low substrate selectivity. A prime example is the bifunctional linalool/nerolidol synthase (LNS) that can use both geranyl diphosphate (GPP) and farnesyl diphosphate (FPP) to produce linalool and nerolidol, respectively.
View Article and Find Full Text PDFGonadal miRNomes and transcriptomes in infected fish reveal sexually dimorphic patterns of the immune response.
Funct Integr Genomics
January 2025
Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (ICM-CSIC), Barcelona, 08003, Spain.
Fish disease outbreaks caused by bacterial burdens are responsible for decreasing productivity in aquaculture. Unraveling the molecular mechanisms activated in the gonads after infections is pivotal for enhancing husbandry techniques in fish farms, ensuring disease management, and selecting the most resilience phenotype. The present study, with an important commercial species the European sea bass (Dicentrarchus labrax), an important commercial species in Europe, examined changes in the miRNome and transcriptome 48 h after an intraperitoneal infection with Vibrio anguillarum.
View Article and Find Full Text PDFDistinct Aggregation Behavior of -Terminally Truncated Aβ Over Aβ in the Presence of Zn(II).
ACS Chem Neurosci
January 2025
Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.
The deposition of amyloid-β (Aβ) aggregates and metal ions within senile plaques is a hallmark of Alzheimer's disease (AD). Among the modifications observed in Aβ peptides, -terminal truncation at Phe4, yielding Aβ, is highly prevalent in AD-affected brains and significantly alters Aβ's metal-binding and aggregation profiles. Despite the abundance of Zn(II) in senile plaques, its impact on the aggregation and toxicity of Aβ remains unexplored.
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