Related papers: TripHLApan: predicting HLA molecules binding pepti…
Many biological processes are governed by protein-ligand interactions. One such example is the recognition of self and nonself cells by the immune system. This immune response process is regulated by the major histocompatibility complex…
The immune checkpoint inhibitors have demonstrated promising clinical efficacy across various tumor types, yet the percentage of patients who benefit from them remains low. The bindings between tumor antigens and HLA-I/TCR molecules…
Major histocompatibility complex class two (MHC-II) molecules are trans-membrane proteins and key components of the cellular immune system. Upon recognition of foreign peptides expressed on the MHC-II binding groove, helper T cells mount an…
The complex nature of tripartite peptide-MHC-TCR interactions is a critical yet underexplored area in immunogenicity prediction. Traditional studies on TCR-antigen binding have not fully addressed the complex dependencies in triad binding.…
T cell receptor (TCR) recognition of peptide-MHC (pMHC) complexes is a central component of adaptive immunity, with implications for vaccine design, cancer immunotherapy, and autoimmune disease. While recent advances in machine learning…
T-cell receptors can recognize foreign peptides bound to major histocompatibility complex (MHC) class-I proteins, and thus trigger the adaptive immune response. Therefore, identifying peptides that can bind to MHC class-I molecules plays a…
T-cells play a key role in adaptive immunity by mounting specific responses against diverse pathogens. An effective binding between T-cell receptors (TCRs) and pathogen-derived peptides presented on Major Histocompatibility Complexes (MHCs)…
The rapidly changing landscape of sequencing technologies brings new opportunities to genomics research. Longer sequence reads and higher sequence throughput coupled with ever-improving base accuracy and decreasing per-base cost is now…
Accurate in silico modeling of the antigen processing pathway is crucial to enable personalized epitope vaccine design for cancer. An important step of such pathway is the degradation of the vaccine into smaller peptides by the proteasome,…
Human leukocyte antigen (HLA) genes are associated with a variety of diseases, however direct typing of HLA is time and cost consuming. Thus various imputation methods using sequential SNPs data have been proposed based on statistical or…
Understanding the binding specificity between T-cell receptors (TCRs) and peptide-major histocompatibility complexes (pMHCs) is central to immunotherapy and vaccine development. However, current predictive models struggle with…
In cancer therapeutics, protein-metal binding mechanisms critically govern the pharmacokinetics and targeting efficacy of drugs, thereby fundamentally shaping the rational design of anticancer metallodrugs. While conventional laboratory…
Traditional vaccines against viruses are designed to target their surface proteins, i.e., antigens, which can trigger the immune system to produce specific antibodies to capture and neutralize the viruses. However, viruses often evolve…
We study the prediction of T-cell response for specific given peptides, which could, among other applications, be a crucial step towards the development of personalized cancer vaccines. It is a challenging task due to limited, heterogeneous…
Personalized vaccines and T-cell immunotherapies depend critically on identifying peptide-MHC class I (pMHC-I) interactions capable of eliciting potent immune responses. However, current benchmarks and models inherit biases present in…
Antibodies have become an important class of therapeutic agents to treat human diseases. To accelerate therapeutic antibody discovery, computational methods, especially machine learning, have attracted considerable interest for predicting…
T cell receptor (TCR) recognition of peptide-MHC (pMHC) complexes is fundamental to adaptive immunity and central to the development of T cell-based immunotherapies. While transformer-based models have shown promise in predicting TCR-pMHC…
T cells monitor the health status of cells by identifying foreign peptides displayed on their surface. T-cell receptors (TCRs), which are protein complexes found on the surface of T cells, are able to bind to these peptides. This process is…
The computational prediction and design of peptide binders targeting specific linear epitopes is crucial in biological and biomedical research, yet it remains challenging due to their highly dynamic nature and the scarcity of experimentally…
Identifying T-cell receptors (TCRs) that interact with antigenic peptides provides the technical basis for developing vaccines and immunotherapies. The emergent deep learning methods excel at learning antigen binding patterns from known…