Computational protocol: Epitope Mapping of Streptococcus agalactiae Elongation Factor Tu Protein Recognized by Human Sera

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Protocol publication

[…] Predictions of epitope regions were made based on sequence analysis. We used Genesilico Metaserver for predictions of secondary structure elements and loop regions, disordered regions, and protein solvation. Additionally, we used web server for epitope localization prediction: Antibody Epitope Prediction applied methods—Emini Surface Accessibility Prediction (), Kolaskar & Tongaonkar Antigenicity () and Bepipred Linear Epitope Prediction (), as another cross method BCPREDS was used from B-cell epitope prediction server. For more detailed predictions, we used homology models made based on 3D structure of PDB: 2C78 [elongation factor Tu (EF-TU) complexed with a GTP analog and the antibiotic pulvomycin]. Based on the 3D structure of the modeled protein, we identified loop regions on the surface of protein with tendency to be disordered and which could be a good epitope. The results obtained were used to make consensus predictions. Any sequences that were positively selected by more than two prediction methods and that contained more than six amino acids were selected as linear epitopes. […]

Pipeline specifications

Software tools BepiPred, BCPREDS
Application Immune system analysis
Organisms Streptococcus agalactiae, Homo sapiens, Bacteria
Diseases Infection, Lymphoma, B-Cell