Computational protocol: The Epitope and Neutralization Mechanism of AVFluIgG01, a Broad-Reactive Human Monoclonal Antibody against H5N1 Influenza Virus

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Protocol publication

[…] Two web-available computer programs, Mapitope and Pep-3D-Search , were applied to predict the AVFluIgG01 epitope based on the selected peptides (mimotopes) from the random phage display library. The algorithm of Mapitope is based on the assumption that the epitope is separated into several amino acid pairs (AAP) contributing for the binding to the antibodies and the entire set of peptides is enriched with AAP which mimic the genuine epitope. In Pep-3D-Search, a promising ACO (Ant Colony Optimization) algorithm was proposed to search matching paths on an antigen surface with respect to the query mimotopes or a motif. Both tools are validated for mapping a conformation-dependent epitope based on the affinity-selected mimotopes. […]

Pipeline specifications

Software tools Mapitope, Pep-3D-Search
Application Immune system analysis
Organisms Homo sapiens
Diseases HIV Infections