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If such a residue does not belong in the interface there is no scoring penalty. Passive residues are those that contribute for the interaction, but are deemed of less importance. Throughout the simulation, these active residues are restrained to be part of the interface, if possible, otherwise incurring in a scoring penalty. Generally, active residues are those of central importance for the interaction, such as residues whose knockouts abolish the interaction or those where the chemical shift perturbation is higher. AIRs are defined through a list of residues that fall under two categories: active and passive. These allow the translation of raw data such as NMR chemical shift perturbation or mutagenesis experiments into distance restraints that are incorporated in the energy function used in the calculations. Moreover, the intimate coupling with CNS endows HADDOCK with the ability to actually produce models of sufficient quality to be archived in the Protein Data Bank.Ī central aspect to HADDOCK is the definition of Ambiguous Interaction Restraints or AIRs.
#PYMOL TUTORIAL CHAIN SOFTWARE#
What distinguishes HADDOCK from other docking software is its ability, inherited from CNS, to incorporate experimental data as restraints and use these to guide the docking process alongside traditional energetics and shape complementarity. HADDOCK (see ) is a collection of python scripts derived from ARIA ( ) that harness the power of CNS (Crystallography and NMR System – ) for structure calculation of molecular complexes.
#PYMOL TUTORIAL CHAIN REGISTRATION#
Use for this the following registration page. In order to run this tutorial you will need to have the following software installed: PyMOL.Īlso, if not provided with special workshop credentials to use the HADDOCK portal, make sure to register in order to be able to submit jobs. This is a question prompt: try answering it! This an instruction prompt: follow it! This is a PyMOL prompt: write this in the PyMOL command line prompt! Throughout the tutorial, coloured text will be used to refer to questions or instructions, and/or PyMOL commands. The local version of PDB-tools can also be found here. pdb-tools: a swiss army knife for molecular structures. proABC-2: PRediction Of AntiBody Contacts v2 and its application to information-driven docking. The HADDOCK web server for data-driven biomolecular docking. The HADDOCK2.2 webserver: User-friendly integrative modeling of biomolecular complexes.
#PYMOL TUTORIAL CHAIN CODE#
In this tutorial we will be working with Interleukin-1β (IL-1β) (PDB code 4I1B)) as an antigen and its highly specific monoclonal antibody gevokizumab (PDB code 4G6K) (PDB code of the complex 4G6M).įor this tutorial we will make use of the HADDOCK2.4 webserver, ProABC-2 and PDB-tools webserver.Ī description of the previous major version of our web server HADDOCK2.2 can be found in the following publications: CDRs are shown in red in the figure below: The paratope consists of six highly flexible loops, known as complementarity-determining regions (CDRs) or hypervariable loops whose sequence and conformation are altered to bind to different antigens.
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The part of the antigen that binds to an antibody is called epitope. The small part of the Fab region that binds the antigen is called paratope. In this tutorial we will concentrate on the terminal variable domain (Fv) of the Fab region. The fragment antigen-binding region (Fab region) needs to be highly variable to be able to bind to antigens of various nature (high specificity). 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.
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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: