A transformer-based model to predict peptide–HLA class I binding and optimize mutated peptides for vaccine design
Human leukocyte antigen (HLA) can recognize and bind foreign peptides to present them to
specialized immune cells, then initiate an immune response. Computational prediction of the …
specialized immune cells, then initiate an immune response. Computational prediction of the …
Unlocking the black box: an in-depth review on interpretability, explainability, and reliability in deep learning
Deep learning models have revolutionized numerous fields, yet their decision-making
processes often remain opaque, earning them the characterization of “black-box” models …
processes often remain opaque, earning them the characterization of “black-box” models …
Peptide-binding specificity prediction using fine-tuned protein structure prediction networks
Peptide-binding proteins play key roles in biology, and predicting their binding specificity is
a long-standing challenge. While considerable protein structural information is available, the …
a long-standing challenge. While considerable protein structural information is available, the …
DisoLipPred: accurate prediction of disordered lipid-binding residues in protein sequences with deep recurrent networks and transfer learning
Motivation Intrinsically disordered protein regions interact with proteins, nucleic acids and
lipids. Regions that bind lipids are implicated in a wide spectrum of cellular functions and …
lipids. Regions that bind lipids are implicated in a wide spectrum of cellular functions and …
Artificial intelligence and neoantigens: paving the path for precision cancer immunotherapy
A Bulashevska, Z Nacsa, F Lang, M Braun… - Frontiers in …, 2024 - frontiersin.org
Cancer immunotherapy has witnessed rapid advancement in recent years, with a particular
focus on neoantigens as promising targets for personalized treatments. The convergence of …
focus on neoantigens as promising targets for personalized treatments. The convergence of …
DeepMHCI: an anchor position-aware deep interaction model for accurate MHC-I peptide binding affinity prediction
Motivation Computationally predicting major histocompatibility complex class I (MHC-I)
peptide binding affinity is an important problem in immunological bioinformatics, which is …
peptide binding affinity is an important problem in immunological bioinformatics, which is …
CapsNet-MHC predicts peptide-MHC class I binding based on capsule neural networks
M Kalemati, S Darvishi, S Koohi - Communications Biology, 2023 - nature.com
Abstract The Major Histocompatibility Complex (MHC) binds to the derived peptides from
pathogens to present them to killer T cells on the cell surface. Developing computational …
pathogens to present them to killer T cells on the cell surface. Developing computational …
Positional SHAP (PoSHAP) for Interpretation of machine learning models trained from biological sequences
Q Dickinson, JG Meyer - PLOS Computational Biology, 2022 - journals.plos.org
Machine learning with multi-layered artificial neural networks, also known as “deep
learning,” is effective for making biological predictions. However, model interpretation is …
learning,” is effective for making biological predictions. However, model interpretation is …
Structure modeling and specificity of peptide-MHC class I interactions using geometric deep learning
A Aronson, T Hochner, T Cohen… - bioRxiv, 2022 - biorxiv.org
Abstract Major Histocompatibility Complex (MHC) plays a major role in the adaptive immune
response by recognizing foreign proteins through binding to their peptides. In humans alone …
response by recognizing foreign proteins through binding to their peptides. In humans alone …
HLAEquity: Examining biases in pan-allele peptide-HLA binding predictors
A Conev, R Fasoulis, S Hall-Swan, R Ferreira… - Iscience, 2024 - cell.com
Peptide-HLA (pHLA) binding prediction is essential in screening peptide candidates for
personalized peptide vaccines. Machine learning (ML) pHLA binding prediction tools are …
personalized peptide vaccines. Machine learning (ML) pHLA binding prediction tools are …