INeo-Epp: A Novel T-Cell HLA Class-I Immunogenicity or Neoantigenic Epitope Prediction Method Based on Sequence-Related Amino Acid Features.

INeo-Epp: A Novel T-Cell HLA Class-I Immunogenicity or Neoantigenic Epitope Prediction Method Based on Sequence-Related Amino Acid Features.
Biomed Res Int. 2020;2020:5798356
Authors: Wang G, Wan H, Jian X, Li Y, Ouyang J, Tan X, Zhao Y, Lin Y, Xie L
Abstract
In silico T-cell epitope prediction plays an important role in immunization experimental design and vaccine preparation. Currently, most epitope prediction research focuses on peptide processing and presentation, e.g., proteasomal cleavage, transporter associated with antigen processing (TAP), and major histocompatibility complex (MHC) combination. To date, however, the mechanism for the immunogenicity of epitopes remains unclear. It is generally agreed upon that T-cell immunogenicity may be influenced by the foreignness, accessibility, molecular weight, molecular structure, molecular conformation, chemical properties, and physical properties of target peptides to different degrees. In this work, we tried to combine these factors. Firstly, we collected significant experimental HLA-I T-cell immunogenic peptide data, as well as the potential immunogenic amino acid properties. Several characteristics were extracted, including the amino acid physicochemical property of the epitope sequence, peptide entropy, eluted ligand likelihood percentile rank (EL rank(%)) score, and frequency score for an immunogenic peptide. Subsequently, a random forest classifier for T-cell immunogenic HLA-I...

Source: Biomed Res - July 8, 2020 Category: Research Authors: Wang G, Wan H, Jian X, Li Y, Ouyang J, Tan X, Zhao Y, Lin Y, Xie L Tags: Biomed Res Int Source Type: research