Toward more accurate pan-specific MHC-peptide binding prediction: a review of current methods and tools

L Zhang, K Udaka, H Mamitsuka… - Briefings in …, 2012 - academic.oup.com
Binding of short antigenic peptides to major histocompatibility complex (MHC) molecules is
a core step in adaptive immune response. Precise identification of MHC-restricted peptides …

Drug side effect prediction through linear neighborhoods and multiple data source integration

W Zhang, Y Chen, S Tu, F Liu… - 2016 IEEE international …, 2016 - ieeexplore.ieee.org
Predicting drug side effects is a critical task in the drug discovery, which attracts great
attentions in both academy and industry. Although lots of machine learning methods have …

Mutated and Bacteriophage T4 Nanoparticle Arrayed F1-V Immunogens from Yersinia pestis as Next Generation Plague Vaccines

P Tao, M Mahalingam, ML Kirtley, CJ van Lier… - PLoS …, 2013 - journals.plos.org
Pneumonic plague is a highly virulent infectious disease with 100% mortality rate, and its
causative organism Yersinia pestis poses a serious threat for deliberate use as a bioterror …

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 …

Designing of Complex Multi-epitope Peptide Vaccine Based on Omps of Klebsiella pneumoniae: An In Silico Approach

T Farhadi, N Nezafat, Y Ghasemi, Z Karimi… - International Journal of …, 2015 - Springer
Klebsiella pneumoniae is a hospital-acquired pathogen that leads to various infections.
There is a great interest in developing an efficient Klebsiella vaccine and epitope-based …

The utility and limitations of current Web-available algorithms to predict peptides recognized by CD4 T cells in response to pathogen infection

FA Chaves, AH Lee, JL Nayak… - The Journal of …, 2012 - journals.aai.org
The ability to track CD4 T cells elicited in response to pathogen infection or vaccination is
critical because of the role these cells play in protective immunity. Coupled with advances in …

Immunodominant T cell determinants of aquaporin-4, the autoantigen associated with neuromyelitis optica

PA Nelson, M Khodadoust, T Prodhomme, C Spencer… - PLoS …, 2010 - journals.plos.org
Autoantibodies that target the water channel aquaporin-4 (AQP4) in neuromyelitis optica
(NMO) are IgG1, a T cell-dependent Ig subclass. However, a role for AQP4-specific T cells in …

Structure-aware deep model for MHC-II peptide binding affinity prediction

Y Yu, L Zu, J Jiang, Y Wu, Y Wang, M Xu, Q Liu - BMC genomics, 2024 - Springer
The prediction of major histocompatibility complex (MHC)-peptide binding affinity is an
important branch in immune bioinformatics, especially helpful in accelerating the design of …

NIEluter: Predicting peptides eluted from HLA class I molecules

Q Tang, F Nie, J Kang, H Ding, P Zhou… - Journal of immunological …, 2015 - Elsevier
The immune system has evolved to make a diverse repertoire of peptides processed from
self and foreign proteomes, which are displayed in antigen-binding grooves of major …

MHC2MIL: a novel multiple instance learning based method for MHC-II peptide binding prediction by considering peptide flanking region and residue positions

Y Xu, C Luo, M Qian, X Huang, S Zhu - BMC genomics, 2014 - Springer
Background Computational prediction of major histocompatibility complex class II (MHC-II)
binding peptides can assist researchers in understanding the mechanism of immune …