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Prediction of Protein Antigen Epitopes from Monoclonal Antibodies by In Silico Molecular Docking

Tânia Maria Manieri1, Gabriela Massaro Barreiros2

  • 1Laboratory of Biopharmaceuticals, Butantan Institute, São Paulo, Brazil. tania.manieri@butantan.gov.br.

Methods in Molecular Biology (Clifton, N.J.)
|May 13, 2026
PubMed

Antibodies are molecules secreted by B lymphocytes, and among the isotypes the most abundant is of the IgG type. Monoclonal antibodies are macromolecules of high affinity and specificity with their receptors, and may have several mechanisms of action and for this reason they are the most studied therapy for the treatment of complex diseases. The characterization of the antigen-antibody interaction is extremely important in understanding the action and efficacy of the antibody. In silico methods are an increasingly growing choice in the evaluation and characterization of these molecules, due to the constant advancement of bioinformatics tools. Through these methods it is possible to predict the paratope of the antibody and the epitope of the antigen and the best interaction between antigen and antibody. The best interaction of the antigen-antibody complex can be performed by docking methods, where from the 3D structure of the antibody and the antigen it is possible to determine the best binding conformation between the molecules.Of the numerous tools currently available, this chapter will focus on free platforms for academic use. It will be described from the obtaining of the 3D structure of the antibody by homology using the ABodyBuilder platform to the docking by the HADDOCK 2.4. Finally, the methodology for identifying binding residues will be described, using the LigPlot+ software.

Keywords:
AntigenDockingEpitopesHaddockIn silicoMonoclonal antibodiesPrediction

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