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Related Concept Videos

Hybridoma Technology01:31

Hybridoma Technology

Hybridoma technology is used for the large-scale production of monoclonal antibodies. Monoclonal antibodies bind to only a single antigenic determinant or epitope. Such antibodies are used in research, diagnostics, and disease therapy. The hybridoma technology established in 1975 by Georges Köhler and Cesar Milstein was awarded the Nobel Prize in Medicine in 1984 for revolutionizing research and therapy.
Hybridoma Selection
Commonly used fusion techniques — electroporation, polyethylene glycol...
Immunogold Electron Microscopy01:20

Immunogold Electron Microscopy

Immunoelectron microscopy utilizes immunogold labeling of endogenous proteins with specific antibodies to detect and localize these proteins in cells and tissues. The procedure provides insights into the distribution and quantification of protein under different stimulation conditions offering clues about their functions. Conjugating highly electron-dense gold particles with primary or secondary antibodies allow antigen detection on and within cells, with high resolution and specificity.

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Related Experiment Video

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A High Throughput MHC II Binding Assay for Quantitative Analysis of Peptide Epitopes
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EpiBuilder: A Tool for Assembling, Searching, and Classifying B-Cell Epitopes.

Renato Simões Moreira1,2, Vilmar Benetti Filho3, Nathália Anderson Calomeno1

  • 1Laboratório de Hemoparasitas e Vetores, Departamento de Produção Animal e Alimentos, Centro de Ciências Agroveterinárias (CAV), Universidade do Estado de Santa Catarina (UDESC), Lages, Brazil.

Bioinformatics and Biology Insights
|May 16, 2022
PubMed
Summary
This summary is machine-generated.

EpiBuilder is a new software tool that aids in assembling, classifying, and searching for linear B-cell epitopes (BCEs) from prediction data. It offers proteome-wide analysis and visualizes epitope characteristics for enhanced immunoinformatics research.

Keywords:
BepiPred-2.0GalaxyImmunoinformatics

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Area of Science:

  • Immunoinformatics
  • Bioinformatics
  • Computational Biology

Background:

  • Epitopes, specific protein regions recognized by antibodies, are crucial in immunoinformatics.
  • Existing tools predict linear B-cell epitopes (BCEs) but lack comprehensive assembly, evaluation, and cross-proteome searching capabilities.

Purpose of the Study:

  • To introduce EpiBuilder, a user-friendly software for post-prediction analysis of BCEs.
  • To facilitate epitope assembly, classification, and proteome-wide searching using BepiPred-2.0 output.
  • To provide a comprehensive tool for epitope characterization and identification across different proteomes.

Main Methods:

  • Developed EpiBuilder software integrating Chou & Fasman beta-turn, Emini surface accessibility, Karplus & Schulz flexibility, Kolaskar & Tongaonkar antigenicity, Parker hydrophilicity, N-glycosylation, and hydropathy predictions.
  • Implemented proteome-wide processing and BLASTP search functionality for identifying sequence variations.
  • Applied EpiBuilder to create epitope datasets for *Trypanosoma brucei gambiense*, *Clostridioides difficile*, and SARS-CoV-2.

Main Results:

  • EpiBuilder provides a user-friendly interface for assembling and classifying predicted epitopes.
  • The software generates unique epitope topologies by integrating multiple predictive features.
  • Proteome-wide searching capabilities enable efficient identification of conserved and variant epitopes.

Conclusions:

  • EpiBuilder significantly enhances the utility of BCE prediction tools by offering essential downstream analysis.
  • The software's comprehensive features and proteome-wide approach streamline epitope discovery and characterization.
  • EpiBuilder serves as a valuable resource for immunoinformatics research, exemplified by its application to diverse pathogens.