相关论文: HLA class I binding prediction via convolutional n…

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…

Human leukocyte antigen (HLA) is an important molecule family in the field of human immunity, which recognizes foreign threats and triggers immune responses by presenting peptides to T cells. In recent years, the synthesis of tumor vaccines…

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 major histocompatibility complex (MHC) class-I pathway supports the detection of cancer and viruses by the immune system. It presents parts of proteins (peptides) from inside a cell on its membrane surface enabling visiting immune cells…

The major histocompatibility complex (MHC) molecules, which bind peptides for presentation on the cell surface, play an important role in cell-mediated immunity. In light of developing databases and technologies over the years, significant…

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…

Proteins play a central role in biology from immune recognition to brain activity. While major advances in machine learning have improved our ability to predict protein structure from sequence, determining protein function from structure…

Predicting peptide--major histocompatibility complex I (pMHC-I) binding affinity remains challenging due to extreme allelic diversity ($\sim$30,000 HLA alleles), severe data scarcity for most alleles, and noisy experimental measurements.…

Protein-protein and protein nucleic acid interactions are vitally important for a wide range of biological processes, including regulation of gene expression, protein synthesis, and replication and assembly of many viruses. We have…

Applying deep learning concepts from image detection and graph theory has greatly advanced protein-ligand binding affinity prediction, a challenge with enormous ramifications for both drug discovery and protein engineering. We build upon…

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)…

Antigenic epitope presented by major histocompatibility complex II (MHC-II) proteins plays an essential role in immunotherapy. However, compared to the more widely studied MHC-I in computational immunotherapy, the study of MHC-II antigenic…

An unsolved challenge in the development of antigen specific immunotherapies is determining the optimal antigens to target. Comprehension of antigen-MHC binding is paramount towards achieving this goal. Here, we present CASTELO, a combined…

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.…

Numerous diseases, particularly autoimmune disorders, are associated with the human leukocyte antigen (HLA), a small genomic region located on human chromosome 6. Adequate characterization of linkage disequilibrium (LD) in the HLA across…

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…

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…

The protein-ligand binding affinity (PLA) prediction goal is to predict whether or not the ligand could bind to a protein sequence. Recently, in PLA prediction, deep learning has received much attention. Two steps are involved in deep…

The human MHC transplantation loci (HLA-A, -B, -C, -DPB1, -DQB1, -DRB1) are the most polymorphic in the human genome. It is generally accepted this polymorphism reflects a role in presenting pathogen-derived peptide to the adaptive immune…

Protein-ligand binding is the process by which a small molecule (drug or inhibitor) attaches to a target protein. Binding affinity, which characterizes the strength of biomolecular interactions, is essential for tackling diverse challenges…