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Epitopes, B-Lymphocyte

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Snowflake: A deep learning-based human leukocyte antigen matching algorithm considering allele-specific surface accessibility.

Frontiers in immunology
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...

NetBCE: An Interpretable Deep Neural Network for Accurate Prediction of Linear B-cell Epitopes.

Genomics, proteomics & bioinformatics
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...

DeepBCE: Evaluation of deep learning models for identification of immunogenic B-cell epitopes.

Computational biology and chemistry
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...

Identifying B-cell epitopes using AlphaFold2 predicted structures and pretrained language model.

Bioinformatics (Oxford, England)
MOTIVATION: Identifying the B-cell epitopes is an essential step for guiding rational vaccine development and immunotherapies. Since experimental approaches are expensive and time-consuming, many computational methods have been designed to assist B-c...

Reverse engineering protection: A comprehensive survey of reverse vaccinology-based vaccines targeting viral pathogens.

Vaccine
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...

Integrated structural proteomics and machine learning-guided mapping of a highly protective precision vaccine against mycoplasma pulmonis.

International immunopharmacology
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...

B cell epitope prediction by capturing spatial clustering property of the epitopes using graph attention network.

Scientific reports
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. ...

An Integrated Approach to Develop a Potent Vaccine Candidate Construct Against Prostate Cancer by Utilizing Machine Learning and Bioinformatics.

Cancer reports (Hoboken, N.J.)
BACKGROUND: Prostate cancer is the most common malignancy among males. Prostaglandin G/H synthase (PGHS) is an essential enzyme in the synthesis of prostaglandins, and its activation has been linked to many malignancies, including colorectal cancer.

VirusImmu: a novel ensemble machine learning approach for viral immunogenicity prediction.

Briefings in functional genomics
The viruses threats provoke concerns regarding their sustained epidemic transmission, making the development of vaccines particularly important. In the prolonged and costly process of vaccine development, the most important initial step is to identif...

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
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...