AIMC Topic: Epitopes, B-Lymphocyte
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AbEpiTope-1.0: Improved antibody target prediction by use of AlphaFold and inverse folding.
Science advances
Jun 13, 2025
B cell epitope prediction tools are crucial for designing vaccines and disease diagnostics. However, predicting which antigens a specific antibody binds to and their exact binding sites (epitopes) remains challenging. Here, we present AbEpiTope-1.0, ...
Multi-Omics Analysis of the virulence factors and designing of next-generation multi-epitopes Vaccines against Rickettsia prowazekii: a computer-aided vaccine designing approach.
Journal of computer-aided molecular design
May 26, 2025
Rickettsia is a genus of bacteria that are obligate intracellular parasites and are responsible for the febrile diseases known collectively as Rickettsioses. The emergence of antibiotic resistance is an escalating concern and thus developing a vaccin...
Multi-criteria decision making and its application to in silico discovery of vaccine candidates for Toxoplasma gondii.
Vaccine
May 15, 2025
Vaccine discovery against eukaryotic parasites is not trivial and few exist. Reverse vaccinology is an in silico vaccine discovery approach, designed to identify vaccine candidates from the thousands of protein sequences encoded by a target genome. P...
Transformer-based deep learning enables improved B-cell epitope prediction in parasitic pathogens: A proof-of-concept study on Fasciola hepatica.
PLoS neglected tropical diseases
Apr 29, 2025
BACKGROUND: The identification of B-cell epitopes (BCEs) is fundamental to advancing epitope-based vaccine design, therapeutic antibody development, and diagnostics, such as in neglected tropical diseases caused by parasitic pathogens. However, the s...
B cell epitope prediction by capturing spatial clustering property of the epitopes using graph attention network.
Scientific reports
Nov 11, 2024
Knowledge of B cell epitopes is critical to vaccine design, diagnostics, and therapeutics. As experimental validation for epitopes is time-consuming and costly, many in silico tools have been developed to computationally predict the B cell epitopes. ...
Integrated structural proteomics and machine learning-guided mapping of a highly protective precision vaccine against mycoplasma pulmonis.
International immunopharmacology
Aug 16, 2024
Mycoplasma pulmonis (M. pulmonis) is an emerging respiratory infection commonly linked to prostate cancer, and it is classified under the group of mycoplasmas. Improved management of mycoplasma infections is essential due to the frequent ineffectiven...
Reverse engineering protection: A comprehensive survey of reverse vaccinology-based vaccines targeting viral pathogens.
Vaccine
Mar 23, 2024
Vaccines have significantly reduced the impact of numerous deadly viral infections. However, there is an increasing need to expedite vaccine development in light of the recurrent pandemics and epidemics. Also, identifying vaccines against certain vir...
DeepBCE: Evaluation of deep learning models for identification of immunogenic B-cell epitopes.
Computational biology and chemistry
Apr 22, 2023
B-Cell epitopes (BCEs) can identify and bind with receptor proteins (antigens) to initiate an immune response against pathogens. Understanding antigen-antibody binding interactions has many applications in biotechnology and biomedicine, including des...
NetBCE: An Interpretable Deep Neural Network for Accurate Prediction of Linear B-cell Epitopes.
Genomics, proteomics & bioinformatics
Dec 13, 2022
Identification of B-cell epitopes (BCEs) plays an essential role in the development of peptide vaccines and immuno-diagnostic reagents, as well as antibody design and production. In this work, we generated a large benchmark dataset comprising 124,879...
Snowflake: A deep learning-based human leukocyte antigen matching algorithm considering allele-specific surface accessibility.
Frontiers in immunology
Jul 29, 2022
Histocompatibility in solid-organ transplantation has a strong impact on long-term graft survival. Although recent advances in matching of both B-cell epitopes and T-cell epitopes have improved understanding of allorecognition, the immunogenic determ...
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