human Fc region should not evoke an immune response in humans. The fragment crystallizable region (Fc region) activates the immune response and is species specific, i.e. Antibodies can be highly specific while showing low immunogenicity, which is achieved by their unique structure. The binding harnesses the immune system to directly attack and destroy the pathogen. We will be following the protocol described in Ambrosetti, et al ArXiv, 2020.Īn antibody is a large protein that generally works by attaching itself to an antigen, which is a unique site of the pathogen. It also includes our newly developed PDB-tools and ProABC-2 webservers. This tutorial demonstrates the use of HADDOCK2.4 for predicting the structure of an antibody-antigen complex. Bonus - using NMR titration data to guide the docking.Scenario 2: A loose definition of the epitope is known.Submission and validation of structures.Scenario 1: No information about the epitope is available.Using HADDOCK to model the antibody-antigen complex.Using PDB tools to renumber the antibody and to extract the variable domain (Fv).Inspecting and preparing the antibody for docking.Using ProABC-2 to identify the paratope.Using PDB tools to extract the amino acid sequence.Extracting antibody amino acid sequence to gain information about the paratope.This tutorial consists of the following sections:
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