These peptides contain previously identified motifs, but also reveal new motifs that are validated by in vitro binding assays. Training of prediction algorithms with yeast-display library data improves the prediction of peptide-binding affinity and the identification of pathogen-associated and tumor-...
While the peptide motifs we observed for HLA-DR401 (Fig. 2d) largely conformed to those observed in previously collected data (Fig. 2e), these motifs did not precisely match those predicted by commonly used MHC-II prediction algorithms, based upon either peptide binding assays, such as NetMHC...
Prediction of MAYV peptide antigens for immunodiagnostic tests by immunoinformatics and molecular dynamics simulationsThe Mayaro virus is endemic to South America, and thepossible involvement ofspp. mosquitoes in its transmission is a risk factor for outbreaks of greater proportions. The virus causes a...
Spacer or linker peptides are strings of amino acids that are inserted within the repeated portions of recombinant proteins in order to separate structurally defined domains while maintaining their function. In the case of repeated multi-epitope (“polytope”) antigens, spacer peptides were originally...
A unified deep framework for peptide–major histocompatibility complex–T cell receptor binding prediction Article Open access 26 February 2025 Deep learning enhances the prediction of HLA class I-presented CD8+ T cell epitopes in foreign pathogens Article Open access 28 January 2025 Data...
Simi- larly, the TGEV B-cell epitope T592SLLASACTIDLFGYP607, which is highly conserved in coronaviruses, can be used as an antigenic peptide for diagnosis (Gebauer et al. 1991). Studies on other coronaviruses indicate that the N protein is highly conserved in different strains. ...
Machine learning (ML) is a key technology for accurate prediction of antibody–antigen binding. Two orthogonal problems hinder the application of ML to antibody-specificity prediction and the benchmarking thereof: the lack of a unified ML formalization of immunological antibody-specificity prediction prob...
In addition to the abovementioned procedure, Proteome Discoverer 1.3 (Thermo, Bremen, Germany) was used to extract all identified peptides from the input *.RAW files, using the Mascot server mentioned above, and calculate their intensity, as reported in supplemental Table S1. False discovery ...
Therefore, prediction of TAP-binding peptides is highly helpful in identifying the MHC class I-restricted T-cell epitopes and hence in the subunit vaccine designing. In this chapter, we describe a support vector machine (SVM)-based method TAPPred that allows users to predict TAP-binding ...
The electrostatic property of CAR surface controlling CAR oligomerization and tonic signaling leads to the prediction that high CAR tonic signaling will be reduced when enhancing the ionic strength in the CAR-T culture medium, considering the fact that the effective charge on proteins in solution coul...