[HTML][HTML] 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 …

Deep learning in proteomics

B Wen, WF Zeng, Y Liao, Z Shi, SR Savage… - …, 2020 - Wiley Online Library
Proteomics, the study of all the proteins in biological systems, is becoming a data‐rich
science. Protein sequences and structures are comprehensively catalogued in online …

A transformer-based model to predict peptide–HLA class I binding and optimize mutated peptides for vaccine design

Y Chu, Y Zhang, Q Wang, L Zhang, X Wang… - Nature Machine …, 2022 - nature.com
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 …

Next-generation computational tools for interrogating cancer immunity

F Finotello, D Rieder, H Hackl, Z Trajanoski - Nature Reviews Genetics, 2019 - nature.com
The remarkable success of cancer therapies with immune checkpoint blockers is
revolutionizing oncology and has sparked intensive basic and translational research into the …

Current challenges for unseen-epitope TCR interaction prediction and a new perspective derived from image classification

P Moris, J De Pauw, A Postovskaya… - Briefings in …, 2021 - academic.oup.com
The prediction of epitope recognition by T-cell receptors (TCRs) has seen many
advancements in recent years, with several methods now available that can predict …

DeepHLApan: a deep learning approach for neoantigen prediction considering both HLA-peptide binding and immunogenicity

J Wu, W Wang, J Zhang, B Zhou, W Zhao, Z Su… - Frontiers in …, 2019 - frontiersin.org
Neoantigens play important roles in cancer immunotherapy. Current methods used for
neoantigen prediction focus on the binding between human leukocyte antigens (HLAs) and …

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 …

[HTML][HTML] ProtInteract: A deep learning framework for predicting protein–protein interactions

F Soleymani, E Paquet, HL Viktor… - Computational and …, 2023 - Elsevier
Proteins mainly perform their functions by interacting with other proteins. Protein–protein
interactions underpin various biological activities such as metabolic cycles, signal …

Synthesis and photoluminescence properties of hybrid 1D core–shell structured nanocomposites based on ZnO/polydopamine

V Fedorenko, R Viter, R Mrówczyński, D Damberga… - RSC …, 2020 - pubs.rsc.org
In the present work, we report on the modelling of processes at the zinc oxide and
polydopamine (ZnO/PDA) interface. The PDA layer was deposited onto ZnO nanorods (NRs) …

Sequence-based peptide identification, generation, and property prediction with deep learning: a review

X Chen, C Li, MT Bernards, Y Shi, Q Shao… - … Systems Design & …, 2021 - pubs.rsc.org
Over the past few years, deep learning has demonstrated itself to be a powerful tool in many
areas, especially bioinformatics. With its previous success in DNA and protein related …