In recent years, the significant role of the human gut microbiota (HGM) in the metabolism of drugs and nutrients has gradually been recognized. The gut microbiota not only affects the bioavailability of orally administered drugs but also participates in the biotransformation of drugs and bioactive molecules through its metabolic enzymes, thereby in...
T-cell receptors (TCRs) play a crucial role in the adaptive immune system by recognizing pathogens through binding to specific antigen epitopes. Understanding the interactions between TCRs and epitopes is essential for uncovering the biological mechanisms of immune responses and developing T cell-mediated immunotherapies. However, although the impo...
Academic Background With the rapid advancement of sequencing technology, scientists have been able to obtain a vast amount of protein sequence data, including many enzyme sequences. However, despite the establishment of large enzyme databases such as the Kyoto Encyclopedia of Genes and Genomes (KEGG) and BRENDA, sequence information for many enzyme...
Plasmids are small, circular, double-stranded DNA molecules that exist independently of chromosomal DNA in bacteria. They facilitate horizontal gene transfer, enabling host bacteria to acquire beneficial traits such as antibiotic resistance and metal resistance. Some plasmids can transfer, replicate, or persist in multiple microorganisms, and these...
Academic Background DNA sequence alignment is a core task in genomics, aiming to map short DNA fragments (reads) to the most probable locations on a reference genome. Traditional methods typically involve two steps: first, indexing the genome, followed by efficient searching to locate potential positions for the reads. However, with the exponential...
The three-dimensional structure of a protein is determined by its amino acid sequence, and the function of the protein is highly dependent on its three-dimensional structure. The side-chain conformations of proteins play a crucial role in protein folding, protein-protein interactions, and de novo protein design. Accurate prediction of protein side-...
Academic Background Cryogenic Electron Microscopy (Cryo-EM) is a crucial experimental technique for determining the structures of macromolecules such as proteins. However, the effectiveness of Cryo-EM is often hindered by noise and missing density values caused by experimental conditions such as low contrast and conformational heterogeneity. Althou...
Research Background Gene Regulatory Networks (GRNs) are crucial tools for understanding the complex biological processes within cells. They reveal the interactions between Transcription Factors (TFs) and target genes, thereby controlling gene transcription and regulating cellular behavior. With the advancement of single-cell RNA sequencing (scRNA-s...
Cancer remains one of the leading causes of death globally. Despite significant advancements in immunotherapy in recent years, such as the successful application of chimeric antigen receptor T-cell (CAR-T) therapy and antibody-drug conjugates (ADCs), the effective identification of cancer-specific surface protein targets remains a major challenge i...
Background Introduction Post-Translational Modifications (PTMs) are crucial mechanisms for regulating cellular activities, including gene transcription, DNA repair, and protein interactions. Among these, cysteine, a rare amino acid, participates in various PTMs through its thiol group, playing a significant role in redox balance and signal transduc...