Challenges in neoantigen-directed therapeutics

L Lybaert, S Lefever, B Fant, E Smits, B De Geest… - Cancer Cell, 2023 - cell.com
A fundamental prerequisite for the efficacy of cancer immunotherapy is the presence of
functional, antigen-specific T cells within the tumor. Neoantigen-directed therapy is a …

Technological advances in cancer immunity: from immunogenomics to single-cell analysis and artificial intelligence

Y Xu, GH Su, D Ma, Y Xiao, ZM Shao… - Signal Transduction and …, 2021 - nature.com
Immunotherapies play critical roles in cancer treatment. However, given that only a few
patients respond to immune checkpoint blockades and other immunotherapeutic strategies …

Peptide-binding specificity prediction using fine-tuned protein structure prediction networks

A Motmaen, J Dauparas, M Baek… - Proceedings of the …, 2023 - National Acad Sciences
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 …

HLAB: learning the BiLSTM features from the ProtBert-encoded proteins for the class I HLA-peptide binding prediction

Y Zhang, G Zhu, K Li, F Li, L Huang… - Briefings in …, 2022 - academic.oup.com
Abstract Human Leukocyte Antigen (HLA) is a type of molecule residing on the surfaces of
most human cells and exerts an essential role in the immune system responding to the …

BERTMHC: improved MHC–peptide class II interaction prediction with transformer and multiple instance learning

J Cheng, K Bendjama, K Rittner, B Malone - Bioinformatics, 2021 - academic.oup.com
Motivation Increasingly comprehensive characterization of cancer-associated genetic
alterations has paved the way for the development of highly specific therapeutic vaccines …

[HTML][HTML] Protein scaffolds in human clinics

O Cano-Garrido, N Serna, U Unzueta, E Parladé… - Biotechnology …, 2022 - Elsevier
Fundamental clinical areas such as drug delivery and regenerative medicine require
biocompatible materials as mechanically stable scaffolds or as nanoscale drug carriers …

A comprehensive assessment and comparison of tools for HLA class I peptide-binding prediction

M Wang, L Kurgan, M Li - Briefings in Bioinformatics, 2023 - academic.oup.com
Human leukocyte antigen class I (HLA-I) molecules bind intracellular peptides produced by
protein hydrolysis and present them to the T cells for immune recognition and response …

Bioactive Molecules from the Innate Immunity of Ascidians and Innovative Methods of Drug Discovery: A Computational Approach Based on Artificial Intelligence

L La Paglia, M Vazzana, M Mauro, A Urso, V Arizza… - Marine Drugs, 2023 - mdpi.com
The study of bioactive molecules of marine origin has created an important bridge between
biological knowledge and its applications in biotechnology and biomedicine. Current studies …

DeepMHCII: a novel binding core-aware deep interaction model for accurate MHC-II peptide binding affinity prediction

R You, W Qu, H Mamitsuka, S Zhu - Bioinformatics, 2022 - academic.oup.com
Motivation Computationally predicting major histocompatibility complex (MHC)-peptide
binding affinity is an important problem in immunological bioinformatics. Recent cutting …

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 …