[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 …

Cancer neoantigens: challenges and future directions for prediction, prioritization, and validation

ES Borden, KH Buetow, MA Wilson… - Frontiers in oncology, 2022 - frontiersin.org
Prioritization of immunogenic neoantigens is key to enhancing cancer immunotherapy
through the development of personalized vaccines, adoptive T cell therapy, and the …

NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand …

B Reynisson, B Alvarez, S Paul, B Peters… - Nucleic acids …, 2020 - academic.oup.com
Major histocompatibility complex (MHC) molecules are expressed on the cell surface, where
they present peptides to T cells, which gives them a key role in the development of T-cell …

Graph convolutional neural networks with global attention for improved materials property prediction

SY Louis, Y Zhao, A Nasiri, X Wang, Y Song… - Physical Chemistry …, 2020 - pubs.rsc.org
The development of an efficient and powerful machine learning (ML) model for materials
property prediction (MPP) remains an important challenge in materials science. While …

Amino acid encoding for deep learning applications

H ElAbd, Y Bromberg, A Hoarfrost, T Lenz, A Franke… - BMC …, 2020 - Springer
Background The number of applications of deep learning algorithms in bioinformatics is
increasing as they usually achieve superior performance over classical approaches …

Artificial intelligence applied in neoantigen identification facilitates personalized cancer immunotherapy

Y Cai, R Chen, S Gao, W Li, Y Liu, G Su, M Song… - Frontiers in …, 2023 - frontiersin.org
The field of cancer neoantigen investigation has developed swiftly in the past decade.
Predicting novel and true neoantigens derived from large multi-omics data became difficult …

PANDORA v2. 0: Benchmarking peptide-MHC II models and software improvements

FM Parizi, DF Marzella, G Ramakrishnan… - Frontiers in …, 2023 - frontiersin.org
T-cell specificity to differentiate between self and non-self relies on T-cell receptor (TCR)
recognition of peptides presented by the Major Histocompatibility Complex (MHC) …

Artificial intelligence-driven systems engineering for next-generation plant-derived biopharmaceuticals

S Parthiban, T Vijeesh, T Gayathri… - Frontiers in Plant …, 2023 - frontiersin.org
Recombinant biopharmaceuticals including antigens, antibodies, hormones, cytokines,
single-chain variable fragments, and peptides have been used as vaccines, diagnostics and …

TransfIGN: A Structure-Based Deep Learning Method for Modeling the Interaction between HLA-A* 02: 01 and Antigen Peptides

N Hong, D Jiang, Z Wang, H Sun, H Luo… - Journal of Chemical …, 2024 - ACS Publications
The intricate interaction between major histocompatibility complexes (MHCs) and antigen
peptides with diverse amino acid sequences plays a pivotal role in immune responses and T …

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 …